Crossover and recombination hotspots massively spread across human genome

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However, most of the recombination hotspots in the human genome are yet to be discovered. We previously reported colonies of CG-rich trinucleotide two-repeat units (CG-TTUs) across the human genome, several of which were shared, with extensive dynamicity, as phylogenetically distant as in mouse. Here we performed a whole-genome analysis of AT-rich trinucleotide two-repeat units (AT-TTUs) in human and found that the majority (96%) resided in approximately 1.4 million colonies, spread throughout the genome. In comparison to the CG-TTU colonies, the AT-TTU colonies were significantly more abundant and larger in size. Pure units and overlapping units of the pure units were readily detectable in the same colonies, signifying that the units are the sites of unequal crossover. Subsequently, we analyzed several of the AT-TTU colonies in several primates and mouse. We discovered dynamic sharedness of several of the colonies across the primate species, which mainly reached maximum complexity and size in human. In conclusion, we report massive crossover and recombination hotspots of the finest molecular resolution and evolutionary relevance in human. In respect of crossover and recombination, the human genome is far more dynamic than previously imagined. Biological sciences/Evolution Biological sciences/Genetics Human AT-rich trinucleotide Two-repeat Unequal crossover Recombination hotspot: Primate Shared Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Introduction Crossover and recombination, alongside mutation, generate the raw material of evolution and speciation 1 , 2 . Recombination hotspots are regions in a genome that exhibit elevated rates of recombination relative to a neutral expectation. Studies on recombination hotspots are mainly founded on mapping crossover events through pedigree analysis and linkage disequilibrium 3 , 4 . Identification of those hotspots paved the way for the discovery of PRDM9, a trimethyl transferase, which is associated with hotspot activity in both humans and mouse 5 – 7 . Using HapMap data, Myers et al. identified a 13-bp “core” motif “CCTCCCTNNCCAC” for PRDM9 binding, which is strongly correlated with hotspot activity when it occurs in both repeat and nonrepeat DNA. A close match to this motif was reported to occur in about 40% of the cross-over hotspots known to date 8 , and degenerate versions of the motif, of variable binding activity for PRDM9, have been identified in the human genome on centimorgan (cM) scales 9 , 10 . The 13-mer motif is the most characterized hotspot locus in human to date. However, the level of expression of PRDM9 should control for only the fraction of targets that are hotspots and the overall temperature of the genome 11 . Other indirect approaches, such as phylogenetic and integrated genetic versus physical map analyses performed by several groups have led to the idea that the local rates of recombination are positively correlated with GC content in the human genome 12 – 15 and a few other mammals 16 . Lined with the above, there are reports that meiotic recombination favors GC-rich alleles over AT-rich alleles, and facilitates local GC-content 17 , 18 . When a meiotic recombination hotspot from a GC-rich isochore was inserted into an AT-rich isochore domain, the site adopted the lower recombination activity, characteristic of its new environment 19 . It is reported that programmed in vitro double strand break formation and loading of axial structure proteins are much more prominent in GC-rich isochores 9 , 10 , 12 . We previously reported that CG-rich trinucleotide two-repeat units (CG-TTUs) form colonies of exceeding significance across the human genome, based on Poisson distribution 20 , 21 . Several of the large and medium size colonies that were further analyzed in other species, unveiled crossover and recombination hotspots, shared across primates, and in some instances, even in mouse. Here, we investigated AT-rich trinucleotide two-repeat units (AT-TTUs) with a similar protocol, and discovered that the colonies formed by AT-TTUs were significantly more abundant and larger than the colonies formed by CG-TTUs. These findings challenge the previous findings of bias towards CG-rich sequences at the recombination hotspots. They also challenge the notion that hotspot loci are rarely (if at all) shared between human and closely related species 11 , 22 – 25 . These novel crossover sites vastly spread across primate genomes, and are there to greatly enhance the resolution of crossover and recombination hotspots at the molecular level. Results The majority of the AT-TTUs resided in colonies. In total, 10,330,879 AT-TTUs were detected genome-wide, of which the majority (9,936,861) (96.18%) were arranged in 1,390,055 colonies (Fig. 1 ). The AT-TTUs were spread across all chromosomes (Fig. 2 ). AT-TTU colonies were significantly more abundant and larger than the CG-TTU colonies. In comparison with the CG-TTU colonies ( https://figshare.com/articles/dataset/All_possible_CGrich_trinucleotides/23260562 ), the colonies formed by AT-TTUs were significantly more abundant (Fig. 3 ). Large intervals of chromosomes were occupied by colony intervals in many chromosomes, for example in chromosome 4. Furthermore, the pattern of distribution of the AT-TTU colonies across human chromosomes was significantly different from the CG-TTU colonies. For example, whereas chromosome 1 had the highest percentage of CG-TTU colonies 21 , AT-TTU colonies reached highest percentage on chromosome 4. Several of the large and medium-size AT-TTU colonies coincided with extensive dynamicity in great apes Several of the large and medium-size AT-TTU colonies in human were also detected in other great apes (Table 1 ). Exceedingly dynamic events were detected across those colonies, affecting the AT-TTUs and the flanking sequences to those units. Across the colonies, the AT-TTUs were either pure or overlaps of two or more pure units. Table 1 Several large and medium-size AT-TTU colonies in human and their corresponding colonies in other primates. Colony Formula b Chr. No. Location (Colony interval) λ value Colony Size in Human a Human Chimpanzee Gorilla Macaque C718 [(ATT)2]32 [(ATA)2]5 [(AAT)2]11 [(TAA)2]2 [(TTA)2]318 [(TAT)2]350 [(ATT)2]21 [(ATA)2]5 [(AAT)2]3 [(TAA)2]2 [(TTA)2]262 [(TAT)2]288 [(ATT)2]3 [(ATA)2]2 [(TAA)2]1 [(TTA)2]4 [(TAT)2]7 11 11:114603789–114625648 75.27 C457 [(ATT)2]13 [(ATA)2]160 [(AAT)2]40 [(TAA)2]43 [(TTA)2]8 [(TAT)2]193 22 22:18728881–18733753 16.78 C350 [(ATT)2]12 [(ATA)2]165 [(AAT)2]15 [(TAA)2]11 [(TTA)2]11 [(TAT)2]136 11 11:96561723–96568076 21.88 C317 [(ATT)2]115 [(ATA)2]59 [(AAT)2]8 [(TAA)2]4 [(TTA)2]14 [(TAT)2]117 [(ATT)2]102 [(ATA)2]47 [(AAT)2]5 [(TAA)2]3 [(TTA)2]12 [(TAT)2]103 12 12:79456025–79468112 41.62 C287 [(ATT)2]11 [(ATA)2]112 [(AAT)2]30 [(TAA)2]13 [(TTA)2]16 [(TAT)2]105 [(ATT)2]2 [(ATA)2]17 [(AAT)2]1 [(TAA)2]1 [(TTA)2]2 [(TAT)2]24 [(ATT)2]2 [(ATA)2]3 [(AAT)2]2 [(TAA)2]1 [(TTA)2]2 [(TAT)2]6 X X:143653179–143659751 22.63 C275 [(ATT)2]6 [(ATA)2]135 [(AAT)2]13 [(TAA)2]10 [(TTA)2]6 [(TAT)2]105 22 22:18891229–18896934 19.65 C267 [(ATT)2]4 [(ATA)2]151 [(AAT)2]4 [(TAA)2]4 [(TTA)2]5 [(TAT)2]99 2 2:16146128–16148756 9.05 C255 [(ATA)2]4 [(AAT)2]247 [(TAA)2]2 [(TTA)2]1 [(TAT)2]1 [(ATA)2]2 [(AAT)2]16 [(TAA)2]1 [(TTA)2]1 [(TAT)2]1 2 2:231822812–231850574 95.60 C212 [(ATA)2]101 [(AAT)2]4 [(TAA)2]6 [(TTA)2]2 [(TAT)2]99 [(ATT)2]20 [(ATA)2]95 [(AAT)2]20 [(TAA)2]16 [(TTA)2]8 [(TAT)2]88 [(ATT)2]1 [(ATA)2]17 [(AAT)2]1 [(TAA)2]3 [(TTA)2]1 [(TAT)2]20 X X: 108772450–108776693 14.61 C200 [(ATT)2]4 [(ATA)2]77 [(AAT)2]76 [(TAA)2]9 [(TTA)2]2 [(TAT)2]32 [(ATT)2]2 [(ATA)2]72 [(AAT)2]70 [(TAA)2]7 [(TTA)2]2 [(TAT)2]30 [(ATA)2]80 [(AAT)2]78 [(TAA)2]10 [(TTA)2]3 [(TAT)2]29 7 7:37785667–37794029 28.80 C198 [(ATT)2]9 [(ATA)2]62 [(AAT)2]14 [(TAA)2]15 [(TTA)2]5 [(TAT)2]93 22 22:18235269–18238724 11.90 C195 [(ATT)2]12 [(ATA)2]61 [(AAT)2]9 [(TAA)2]6 [(TTA)2]15 [(TAT)2]92 [(ATT)2]10 [(ATA)2]48 [(AAT)2]3 [(TAA)2]4 [(TTA)2]10 [(TAT)2]58 [(ATT)2]6 [(ATA)2]31 [(AAT)2]4 [(TAA)2]4 [(TTA)2]4 [(TAT)2]17 10 10:67724852–67731164 21.74 C190 [(ATT)2]2 [(ATA)2]38 [(AAT)2]5 [(TAA)2]6 [(TTA)2]3 [(TAT)2]136 2 2:194462444–194465074 9.06 C184 [(ATT)2]34 [(ATA)2]18 [(AAT)2]30 [(TAA)2]4 [(TTA)2]61 [(TAT)2]37 [(ATT)2]23 [(ATA)2]10 [(AAT)2]19 [(TAA)2]3 [(TTA)2]34 [(TAT)2]24 [(ATT)2]19 [(ATA)2]10 [(AAT)2]17 [(TAA)2]2 [(TTA)2]26 [(TAT)2]19 [(ATT)2]6 [(ATA)2]1 [(AAT)2]3 [(TAA)2]1 [(TTA)2]2 [(TAT)2]5 6 6:77601972–77604184 7.62 C182 [(ATT)2]13 [(ATA)2]51 [(AAT)2]17 [(TAA)2]16 [(TTA)2]12 [(TAT)2]73 [(ATT)2]6 [(ATA)2]65 [(AAT)2]12 [(TAA)2]11 [(TTA)2]9 [(TAT)2]38 [(ATT)2]4 [(ATA)2]31 [(AAT)2]2 [(TAA)2]2 [(TTA)2]6 [(TAT)2]22 [(ATT)2]3 [(ATA)2]11 [(AAT)2]2 [(TAA)2]3 [(TTA)2]7 [(TAT)2]15 14 14:52527096–52531874 16.45 C175 [(ATT)2]5 [(ATA)2]68 [(AAT)2]5 [(TAA)2]7 [(TTA)2]23 [(TAT)2]67 7 7:54395223–54397576 8.10 C173 [(ATA)2]69 [(AAT)2]64 [(TAA)2]18 [(TAT)2]22 16 16:18565943–18570325 15.09 C161 [(ATT)2]68 [(ATA)2]17 [(AAT)2]2 [(TAA)2]2 [(TTA)2]8 [(TAT)2]64 [(ATT)2]65 [(ATA)2]17 [(AAT)2]2 [(TAA)2]2 [(TTA)2]8 [(TAT)2]64 [(ATT)2]68 [(ATA)2]17 [(AAT)2]3 [(TAA)2]2 [(TTA)2]4 [(TAT)2]65 3 3:8693642–8702099 29.12 a Colony size, chromosomal location, colony interval, and λ value are based on the human genome, as reference. The corresponding colonies in other species were identified, using BLASTN. Instances in which the colonies were partially or not sequenced (such as C287, C212, and C200 in gorilla), or lacked the corresponding colony in a species were left blank. Poisson probability values for all the colony sizes in this table is inherent zero. None of the colonies in this table were detected in mouse lemur or mouse. b Formulas represent absolute numbers of units, regardless of being pure or overlapping. The largest AT-TTU colony in human was a compound colony of 718 units (C718), located on chromosome 11, which was detected with exceeding dynamicity in human and chimpanzee, and at a far lesser extent in gorilla. This colony reached maximum complexity and size in human (Fig. 4 ). The absolute number of the AT-TTUs and the distribution of the units in the pure and overlapping compartments were exceedingly dynamic across those species, adding multiple layers of complexity of the events, and leading to massively divergent compositions. Most of the units in C718 and its orthologous colonies were in the overlapping compartment (Figs. 4 and 5 A). Furthermore, the immediate flanking sequences of the units were significantly dynamic with respect to mutations (Fig. 5 B). Models proposed for the evolution of pure and overlapping units. Some of the pure units were the inverted or palindromic sequences of one another, and probably emerged, and resulted in DNA breakage and recombination events inherent to inverted and palindromic sequences, for example, two pure units of TTATTA and ATTATT (inversion), and TTATTA and TAATAA (palindrome). Overlapping units were a consequence of unequal crossovers among the pure units. For example, in C718, the most prevalent overlapping unit, TTATTAT, was the consequence of unequal crossovers between pure units, TTATTA and TATTAT (Fig. 5 A). In another example in C718, the overlapping unit, AATAATTATTAT, was the consequence of several unequal crossovers across units (Fig. 5 A). It is conceivable that reverse processes leading to the overlapping units could result in the re-emergence of the pure units. The flanking sequences of the units were also highly dynamic (Fig. 5 B), signifying the occurrence of crossovers at the sites of the AT-TTUs, and coupled breakage and repair at, and around these sites. Coi ncidence of some of the colonies beyond great apes. Several colonies, such as C212, C200, and C184 coincided beyond great apes, and included macaque (Table 1 ). As an example, in C184, the colonies were shared dynamically in human, chimpanzee, gorilla, and macaque, and there was a directional incremented trend of complexity of the events and units in human (Fig. 6 ). Pure and overlapping units were also detected across this colony in human and other primates. For example, TATTATTA, was the consequence of unequal crossovers between TATTAT, ATTATT, and TTATTA pure units. Colonies that were detected in human and not the other five species studied. We also detected colonies that were found in human only (Table 1 ), such as C457 (Fig. 7 A) and C190 (Fig. 7 B). we detected strings of consecutive pure units recombining with each other, or pure and overlapping units recombining with each other. AT-TTUs are a mechanism for the emergence of AT short tandem repeats (STRs). The AT-TTUs and coupled unequal crossovers and recombination at these sites result in the emergence of STRs (repeats of ≥ 3). For example, in C184, the (TTA)3 STR could be a consequence of unequal crossovers through various paths (Fig. 8 A and B). In other examples, in C457 and C190, unequal crossovers gave rise to overlapping units for the emergence of several (ATA)3 STRs (Fig. 8 C,D, and E). We detected the pure units and intermediate overlapping units necessary for the emergence of STRs in the same (or orthologous) colonies that the STRs were detected. Discussion The bulk of literature is dominated by reports of the preference of CG- over AT-rich sequences at the recombination hotspots 15 , 26 – 31 . Limited reports of the involvement of AT-rich sequences in recombination and consequent translocations are available in the literature, which primarily concern AT-rich palindromic or inverted sequences. Those events are mainly involved in chromosomal translocations and deletions, for example in chromosomes 11, 17, and 22 32–34 . Here, we report a phenomenon, in which AT-TTUs colonize across the genome with exceedingly significant Poisson probability values. In fact, the majority of AT-TTUs in the human genome reside in colonies, and those colonies span significant intervals of several chromosomes. The AT-TTU colonies were significantly larger and more complex than the CG-rich colonies that we reported previously 20 , 21 . These findings support a more significant role of AT-rich sequences in comparison with CG-rich sequences, as crossover and recombination hotspots. While the AT-TTU crossover hotspots were ubiquitous, the most refined maps of recombination identified so far are on the scales of cM 35 , 36 . The presence of pure units and overlapping units of those pure units, and the fact that the common elements across the colonies were the AT-TTUs, signify that the main reason for the hotspot events in those colonies is the AT-TTUs, and not their flanking sequences. The inversions and palindromes as a result of the pure and overlapping units increase the rate of various genetic rearrangement events and recombination across the colonies. Palindromes and inversions are known to be recombinogenic in the genomes, and a risk to instability 37 , 38 . The flanking sequences of the AT-TTUs were also extensively dynamic. The very high dynamicity of the flanking sequences was in line with the previous reports that flanking sequences to the recombination sites are prone to mutations 39 , 36 . Some of the identified colonies, which were further studied in other primates, were shared in those primates with exceeding dynamicity of the events. These findings challenge the long-lasting literature on the rarity of shared recombination hotspots between human and closely related species 22 – 25 . An isolate report of shared hotspot loci between human and chimpanzee was at β-globin and HLA regions on chromosome 21, which was based on high Bayes factors of shared hotspots at locations within both regions 40 . Our data extend crossover and recombination hotspot sharedness across primates, and envision a new perspective in the field, with respect to mechanistic, evolutionary, and magnitude of crossovers and recombination. It is reasonable to consider the AT-TTUs a novel genomic entity, as although they are repeats, they do not conform to the conventional definition of repetitive DNA sequences, such as microsatellites and minisatellites 41 . Neither the well-characterized recombination hotspot 13-mer, nor the degenerate sequences of this sequence could explain the identified colonies and the extent of the events occurring across those colonies. In comparison with CG-TTU colonies, the AT-TTU colonies (at least the colonies that were further analyzed in additional primates), were mainly more complex in human, at a directional trend. Furthermore, the rate of detecting those colonies in human only (in comparison with the other species that were studied) was higher than the CG-TTU colonies 21 . One explanation may be that the mechanisms involved in the AT-TTU colonies have evolved more recently than the CG-TTU colonies. This is also supported by the fact that we could not identify AT-TTU orthologous colonies in mouse lemur and mouse, whereas in the instance of CG-TTU colonies, several of the colonies were identified in those species 21 . The AT-TTUs and the crossovers coupled with those units are a novel mechanism for the emergence of STRs. This follows from our observations that all the pure and intermediate overlapping units necessary for the birth and maturation of a given STR were detectable in the same (or orthologous) colonies. The evolutionary, biological, and pathological implications of STRs are an emerging topic of research among others 42 – 45 . In summary, in view of the events and mechanisms associated with the identified units, their abundance and ubiquity throughout the genomes studied, and their exceedingly significant colonization based on Poisson distribution, we predict these units of phenomenal evolutionary and biological consequences. However, this is the tip of the iceberg, and the evolutionary purpose of this phenomenon is yet to be discovered in the future studies. Conclusion In conclusion, our findings unveil massive AT-TTUs as crossover and recombination hotspots in human and several other primates. These findings challenge the hypothesis that CG-rich sequences are preferred over AT-rich sequences at the crossover and recombination hotspots. Our findings also unveil sharedness of these hotspots, at least across great apes and Old-World monkeys, and challenge once again, the hypothesis that human and closely related species do not share recombination hotspots. AT-TTUs are a novel mechanism for the emergence of STRs across species. We propose that, with respect to crossovers and recombination, genomes of primates are far more dynamic than previously imagined. Methods Whole-genome extraction of AT-TTUs in human. A Java software package was created (available at https://github.com/arabfard/Java_STR_Finder ) to facilitate the extraction of specific type of DNA sequence units, known as AT-TTUs, including AATAAT, ATAATA, ATTATT, TTATTA, TATTAT, and TAATAA, along with their corresponding locations. To ensure the accuracy and reliability of the data obtained from the algorithm, a validation process was conducted. This involved randomly examining these units across the entire genome. By manually inspecting the identified units, we were able to detect any potential errors or false positives generated by the algorithm. Through this verification process, we confirmed that the algorithm functioned as intended, and produced reliable results. In order to extract all AT-TTUs, we utilized the latest version of the human genome assembly (GRCh38. p14) obtained from the UCSC genome browser (accessible at https://hgdownload.soe.ucsc.edu ). Comparison of the AT-TTU versus CG-TTU colonies in the human genome. The AT-TTU colonies from the present study were compared with the CG-TTU colonies, yielded from our previous study 21 , https://figshare.com/articles/dataset/All_possible_CG-rich_trinucleotides/23260562 . The extraction algorithm The developed Java program was used to extract all possible AT-TTUs, as follows: AATAAT, ATAATA, ATTATT, TTATTA, TATTAT, and TAATAA, from the human genome sequence. The program initiated its search from the first nucleotide of the genome, continuously scanning for duplicated occurrences of AT-rich trinucleotide cores. It employed a window frame consisting of 6 nucleotides to identify instances of the core sequence repeating twice. Upon discovering a unit, the program recorded the number and location of the two-repeat occurrences. It then proceeded to search for new AT-TTUs, starting from the next nucleotide. To validate the results, the final list of identified AT-TTUs underwent manual evaluation, using the Ensembl genome browser 109 ( https://asia.ensembl.org/index.html ). The precise locations of the AT-TTUs were determined as follows: The output was organized and classified in an Excel file, where the start and end points of each unit were determined within the genome. By subtracting the start and end points of subsequent units, colonies were identified. If the resulting distance was less than 500 bp, the units were considered part of the same colony. Subsequently, a list of colonies consisting of two or more units was compiled, the total count of colonies was determined, and the output was saved in a readily available format ( https://doi.org/10.6084/m9.figshare.24202461.v1 ). Screening several of the large and medium-size human colonies in other species The Ensembl Genome Browser 109 was utilized to conduct a comparative analysis of various size colonies in human and several other species, including chimpanzee, gorilla, macaque, mouse lemur, and mouse (Table 1 ). The analysis involved employing the BLASTN program available on the Ensembl Genome Browser 109 ( https://asia.ensembl.org/index.html ). Statistical analysis To assess the significance of differences between two frequency groups, the Wilcoxon Signed-Rank Test was employed. We utilized the Poisson distribution to determine the λ value and probability distribution of various size colonies (Table 1 ). The Poisson distribution is commonly used to model the occurrence of rare events within a given interval. In our study, we applied this distribution to model the occurrence of AT-TTUs of all possible AT-rich trinucleotide units in the human genome. This modeling considers the average number of units in an interval, which is proportional to the interval's length. The Poisson process assumes that the occurrence of these units is random and independent of each other. Furthermore, it assumes that their distribution across the genome is relatively uniform. In order to calculate the probability of units in the colony occurrence, using the Poisson density function, we needed to determine the expected number of units per colony interval of the genome. This involved dividing the total number of identified colonies by the total length of the genome and applying a correction factor to account for the expected number of colonies. By applying the Poisson distribution, we were able to calculate the probability of the number of different units, occurring in a given colony. This calculation was performed, using the Poisson density function, with specific parameters that capture the characteristics of the distribution and the expected rate of unit occurrence in the colony. $${\lambda }=\frac{Colony Interval \text{*}\text{a}\text{l}\text{l} \text{p}\text{o}\text{s}\text{s}\text{i}\text{b}\text{l}\text{e} \text{u}\text{n}\text{i}\text{t}\text{s} \text{o}\text{f} \text{A}\text{T}-\text{r}\text{i}\text{c}\text{h} \text{t}\text{r}\text{i}\text{n}\text{u}\text{c}\text{l}\text{e}\text{o}\text{t}\text{i}\text{d}\text{e}\text{s} \text{i}\text{n} \text{t}\text{h}\text{e} \text{g}\text{e}\text{n}\text{o}\text{m}\text{e} }{3000000000\left(3\text{g}\text{b}\right)}$$ For example, the largest colony, C718, spanned 21,859 bases. On the other hand, the total number of AT-TTUs in the human genome was about 10,330,879, resulting in λ = 75.27 for the C718 colony, meaning that based on the Poisson distribution, the average expected count of AT-TTUs in the 21,859 interval was 75.27. Table 1 presents values of λ for several colony sizes, the calculated probability of all of which was inherent zero. Visualization The six pure AT-TTUs were visualized as: TTATTA , TATTAT , AATAAT , ATTATT , ATAATA , and TAATAA . The overlapping units were also highlighted, using various highlight and text colors. Abbreviations AT-TTU AT-rich Trinucleotide Two-repeat Unit C: Colony CG-TTU CG-rich Trinucleotide Two-repeat Unit STR Short Tandem Repeat Declarations Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Acknowledgments: Not applicable. Funding: Not applicable. Author contributions: Conceptualization: MO Methodology: MA Investigation: MA, SKh, SA, SV, HB, NT Visualization: MA, SA, SKh Project administration: MO, AD, HRKh Supervision: MO Writing – original draft: MO, MA Writing – review & editing: MO, MA, HO Competing interests: None to be declared. Data and materials availability: Raw data for AT-TTUs are available at the following link: https://figshare.com/articles/dataset/AT-rich_trinucleotides/24202461 Raw data for CG-TTUs are available at the following link: https://figshare.com/articles/dataset/All_possible_CG-rich_trinucleotides/23260562 References Ortiz-Barrientos, D., Engelstadter, J. & Rieseberg, L. H. Recombination Rate Evolution and the Origin of Species. Trends Ecol Evol 31, 226–236, doi: 10.1016/j.tree.2015.12.016 (2016). Paigen, K. & Petkov, P. Mammalian recombination hot spots: properties, control and evolution. Nat Rev Genet 11, 221–233, doi: 10.1038/nrg2712 (2010). Wall, J. D. & Stevison, L. S. 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Comparative recombination rates in the rat, mouse, and human genomes. Genome Res 14, 528–538, doi: 10.1101/gr.1970304 (2004). Duret, L. & Galtier, N. Biased gene conversion and the evolution of mammalian genomic landscapes. Annu Rev Genomics Hum Genet 10, 285–311, doi: 10.1146/annurev-genom-082908-150001 (2009). Marsolier-Kergoat, M. C. & Yeramian, E. GC content and recombination: reassessing the causal effects for the Saccharomyces cerevisiae genome. Genetics 183, 31–38, doi: 10.1534/genetics.109.105049 (2009). Charlesworth, D. et al. Using GC Content to Compare Recombination Patterns on the Sex Chromosomes and Autosomes of the Guppy, Poecilia reticulata, and Its Close Outgroup Species. Mol Biol Evol 37, 3550–3562, doi: 10.1093/molbev/msaa187 (2020). Kurahashi, H. et al. Molecular cloning of a translocation breakpoint hotspot in 22q11. Genome Res 17, 461–469, doi: 10.1101/gr.5769507 (2007). Bi, W. et al. Reciprocal crossovers and a positional preference for strand exchange in recombination events resulting in deletion or duplication of chromosome 17p11.2. Am J Hum Genet 73, 1302–1315, doi: 10.1086/379979 (2003). Edelmann, L. et al. AT-rich palindromes mediate the constitutional t(11;22) translocation. Am J Hum Genet 68, 1–13, doi: 10.1086/316952 (2001). Spence, J. P. & Song, Y. S. Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations. Sci Adv 5, eaaw9206, doi: 10.1126/sciadv.aaw9206 (2019). Pratto, F. et al. DNA recombination. Recombination initiation maps of individual human genomes. Science 346, 1256442, doi: 10.1126/science.1256442 (2014). Svetec Miklenic, M. & Svetec, I. K. Palindromes in DNA-A Risk for Genome Stability and Implications in Cancer. Int J Mol Sci 22, doi: 10.3390/ijms22062840 (2021). Flores, M. et al. Recurrent DNA inversion rearrangements in the human genome. Proc Natl Acad Sci U S A 104, 6099–6106, doi: 10.1073/pnas.0701631104 (2007). Kiktev, D. A., Sheng, Z., Lobachev, K. S. & Petes, T. D. GC content elevates mutation and recombination rates in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 115, E7109-E7118, doi: 10.1073/pnas.1807334115 (2018). Wang, Y. & Rannala, B. Bayesian inference of shared recombination hotspots between humans and chimpanzees. Genetics 198, 1621–1628, doi: 10.1534/genetics.114.168377 (2014). Lower, S. E., Dion-Cote, A. M., Clark, A. G. & Barbash, D. A. Special Issue: Repetitive DNA Sequences. Genes (Basel) 10, doi: 10.3390/genes10110896 (2019). Maddi, A. M. A., Kavousi, K., Arabfard, M., Ohadi, H. & Ohadi, M. Tandem repeats ubiquitously flank and contribute to translation initiation sites. BMC Genom Data 23, 59, doi: 10.1186/s12863-022-01075-5 (2022). Arabfard, M. et al. Global abundance of short tandem repeats is non-random in rodents and primates. BMC Genom Data 23, 77, doi: 10.1186/s12863-022-01092-4 (2022). Horton, C. A. et al. Short tandem repeats bind transcription factors to tune eukaryotic gene expression. Science 381, eadd1250, doi: 10.1126/science.add1250 (2023). Alizadeh, S. et al. A GCC repeat in RAB26 undergoes natural selection in human and harbors divergent genotypes in late-onset Alzheimer's disease. Gene 893, 147968, doi: 10.1016/j.gene.2023.147968 (2024). Additional Declarations No competing interests reported. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-3859914","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":268248615,"identity":"61a6e0d3-506a-4f6f-9698-e7d1bf1ef63c","order_by":0,"name":"Mina Ohadi","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA0UlEQVRIiWNgGAWjYDACCSBKYGDgYWBgPsDA2ECaFrYEErRAWDwGxGnhl25+eOMBwzYZc/Yz3yR+7rCRY2A/fHQDPi2Sc44ZWyQw3Oax7MndJtl7Js2YgSct7QY+LQY3EswkQFoMDuRuk+BtO5zYIMFjRkBL+jeIlvNvnkn+JU5LDtSWGzls0kTZIjkjp9giwQCk5ZmxtWxbmjEbIb/wS6RvvPmj4ra9wfnkhzffttnI8bMfPoZXC9R5YJIFHEFshJUjAPMHUlSPglEwCkbByAEAHv1JDnwXSuIAAAAASUVORK5CYII=","orcid":"","institution":"Iranian Research Center on Aging, University of Social Welfare and Rehabilitation","correspondingAuthor":true,"prefix":"","firstName":"Mina","middleName":"","lastName":"Ohadi","suffix":""},{"id":268248616,"identity":"82b96623-6420-448b-8691-b2a320891c32","order_by":1,"name":"Masoud Arabfard","email":"","orcid":"","institution":"Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences","correspondingAuthor":false,"prefix":"","firstName":"Masoud","middleName":"","lastName":"Arabfard","suffix":""},{"id":268248617,"identity":"5cca4323-21d2-401c-b134-39ae9b222def","order_by":2,"name":"Safoura Khamse","email":"","orcid":"","institution":"Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.","correspondingAuthor":false,"prefix":"","firstName":"Safoura","middleName":"","lastName":"Khamse","suffix":""},{"id":268248618,"identity":"4913acb7-047d-4e46-b9ff-15fda48c2e5f","order_by":3,"name":"Samira Alizadeh","email":"","orcid":"","institution":"Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.","correspondingAuthor":false,"prefix":"","firstName":"Samira","middleName":"","lastName":"Alizadeh","suffix":""},{"id":268248619,"identity":"8d8bbcfb-0399-4f96-82dc-4311466dad7d","order_by":4,"name":"Sara Vafadar","email":"","orcid":"","institution":"Iranian Research Center on Aging, University of Social Welfare and Rehabilitation","correspondingAuthor":false,"prefix":"","firstName":"Sara","middleName":"","lastName":"Vafadar","suffix":""},{"id":268248620,"identity":"b220116b-6238-4808-bce8-054583f80eb1","order_by":5,"name":"Hadi Bayat","email":"","orcid":"","institution":"Iranian Research Center on Aging, University of Social Welfare and Rehabilitation","correspondingAuthor":false,"prefix":"","firstName":"Hadi","middleName":"","lastName":"Bayat","suffix":""},{"id":268248621,"identity":"b48c6b19-e203-42ef-81a1-2e8ca3e9ba07","order_by":6,"name":"Hamid Ohadi","email":"","orcid":"","institution":"University of St Andrews","correspondingAuthor":false,"prefix":"","firstName":"Hamid","middleName":"","lastName":"Ohadi","suffix":""},{"id":268248622,"identity":"bc030c41-a7b7-4a00-b469-2bcfd4ebcaa0","order_by":7,"name":"Nahid Tajeddin","email":"","orcid":"","institution":"Iranian Research Center on Aging, University of Social Welfare and Rehabilitation","correspondingAuthor":false,"prefix":"","firstName":"Nahid","middleName":"","lastName":"Tajeddin","suffix":""},{"id":268248623,"identity":"34e5981c-4dbd-4e2a-910c-11c3bd03acd9","order_by":8,"name":"Ali Maddi","email":"","orcid":"","institution":"Institute of Biochemistry and Biophysics (IBB), University of Tehran","correspondingAuthor":false,"prefix":"","firstName":"Ali","middleName":"","lastName":"Maddi","suffix":""},{"id":268248624,"identity":"62b90041-7b1c-4a22-a23f-e6c396442b1d","order_by":9,"name":"Ahmad Delbari","email":"","orcid":"","institution":"Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.","correspondingAuthor":false,"prefix":"","firstName":"Ahmad","middleName":"","lastName":"Delbari","suffix":""},{"id":268248625,"identity":"9aaa5808-bcdb-4291-b60c-56b02952516c","order_by":10,"name":"Hamid Reza Khorram Khorshid","email":"","orcid":"","institution":"Personalized Medicine and Genometabolomics Research Center, Hope Generation Foundation, Tehran, Iran.","correspondingAuthor":false,"prefix":"","firstName":"Hamid","middleName":"Reza Khorram","lastName":"Khorshid","suffix":""}],"badges":[],"createdAt":"2024-01-13 11:14:08","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-3859914/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-3859914/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":49950204,"identity":"70f17e99-06eb-4208-8525-ce509565bff5","added_by":"auto","created_at":"2024-01-22 06:02:08","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":24369,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eGenome-wide abundance of AT-TTUs in human. \u003c/strong\u003eThe count of all detected AT-TTUs in colonies versus genome-wide is depicted. The majority of the units were arranged in colonies. Absolute counts are depicted.\u003c/p\u003e","description":"","filename":"F1.png","url":"https://assets-eu.researchsquare.com/files/rs-3859914/v1/7ac9bbb83f9355737bd6aaff.png"},{"id":49950205,"identity":"739c8bea-c5ff-4056-85a3-b841d84a4126","added_by":"auto","created_at":"2024-01-22 06:02:08","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":49431,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eCount of AT-TTUs across human chromosomes. \u003c/strong\u003eChromosome-by-chromosome absolute count of all possible AT-TTUs is depicted. AT-TTU=AT-rich trinucleotide two-repeat unit.\u003c/p\u003e","description":"","filename":"F2.png","url":"https://assets-eu.researchsquare.com/files/rs-3859914/v1/0c9ea7c506f39a92790f6908.png"},{"id":49950207,"identity":"6d32c18b-79c1-42cc-b545-318cf4b754c8","added_by":"auto","created_at":"2024-01-22 06:02:08","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":40806,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eNormalized distribution of AT-TTU versus CG-TTU colonies across human chromosomes.\u003c/strong\u003e The CG-TTU data were extracted from the following link: \u003ca href=\"https://figshare.com/articles/dataset/All_possible_CG-rich_trinucleotides/23260562\"\u003ehttps://figshare.com/articles/dataset/All_possible_CG-rich_trinucleotides/23260562\u003c/a\u003e. The AT-TTU colonies were significanlty more abundant than the CG-TTU colonies, and occupied significant intervals of several chromosomes, such as chromosome 4.\u003c/p\u003e","description":"","filename":"F3.png","url":"https://assets-eu.researchsquare.com/files/rs-3859914/v1/e0617fa7139ae0a0c45f57c9.png"},{"id":49950206,"identity":"30d7641b-e09b-4fda-9616-d9769bafa4fa","added_by":"auto","created_at":"2024-01-22 06:02:08","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":628973,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eThe largest AT-TTU colony in human (C718) and the corresponding colonies in chimpanzee and gorilla.\u003c/strong\u003e While the colony was shared across these apes, we detected dynamic differences and species-specific formulas and compositions due to crossovers and flanking mutations. Pure units and overlapping units of those pure units were detectable, signifying sites of unequal cross-over at the units. The colony reached maximum complexity and size in human.\u003c/p\u003e","description":"","filename":"F4.png","url":"https://assets-eu.researchsquare.com/files/rs-3859914/v1/07bf2626669218427d0b22c3.png"},{"id":49950210,"identity":"2dd7d529-3e19-4fae-a21c-00259843337c","added_by":"auto","created_at":"2024-01-22 06:02:08","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":162642,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eEmergence of overlapping units from pure units.\u003c/strong\u003e Emergence of the most prevalent overlapping unit in C718, and other overlapping units in this colony \u003cstrong\u003eA). \u003c/strong\u003eFor simplicity, only the alleles involved in the process of gaining overlapping units are depicted. A sample of the flanking sequences to each unit is depicted, which represent high density of mutations at these nucleotides \u003cstrong\u003eB)\u003c/strong\u003e. For the units that were highly prevalent, only 10 sequences were randomly selected from the human C718 colony. Underlines represent mutations (the least frequent substitutions in a given nucleotide position are underlined). The high density of flanking mutations is an expected consequence of the unequal crossovers at the units and breakage/repair mechanisms at, and around these sites. The models represent only a sample of the dynamicity at the units and their flanking sequences.\u003c/p\u003e","description":"","filename":"F5.png","url":"https://assets-eu.researchsquare.com/files/rs-3859914/v1/18f144f0e100c1bb8658fbcf.png"},{"id":49950363,"identity":"7cac1f77-19b9-44de-a5d3-4ab734ba5038","added_by":"auto","created_at":"2024-01-22 06:10:08","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":211144,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eExample colony shared across great apes and macaque (C184). \u003c/strong\u003eHigh dynamicity encompassed the AT-TTUs, as well as the flanking sequences to each unit. The colony reached maximum complexity and size in human. It is conceivable that the pure units, AATAAT and TTATTA, emerged from unequal crossovers between sister chromatids and non-sister homologous chromosomes. It can also be predicted that AATAAT emerged before TTATTA, as the former was detectable as distantly as in macaque, whereas TTATTA was not detected in this species. Overlapping units of these units and other pure units later emerged in gorilla, chimpanzee, and human.\u003c/p\u003e","description":"","filename":"F6.png","url":"https://assets-eu.researchsquare.com/files/rs-3859914/v1/7c1cd0c18c3a0e3989e9332a.png"},{"id":49950209,"identity":"fc6dbe0b-7056-4924-a735-b9ef59a08beb","added_by":"auto","created_at":"2024-01-22 06:02:08","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":499831,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eExample colonies that were detected in human and not the other five species. \u003c/strong\u003eThese colonies were denser than the non-specific colonies. \u003cstrong\u003eA)\u003c/strong\u003e C457 was the largest colony in the human-only category. The density of the unequal crossovers in C457 was so high that we detected recombination of several pure and overlapping units in some regions, e.g., consecutive recombination of blue, purple, and navy units. Inversions and palindromes were readily detectable. For example, the ATAATATATTAT palindrome was the consequence of the recombination of two pure units, ATAATA and TATTAT. \u003cstrong\u003eB)\u003c/strong\u003e C190 exemplifies a middle size colony of mainly pure units. This colony was also highly dynamic with respect to the intensity of AT-TTU crossovers.\u003c/p\u003e","description":"","filename":"F7.png","url":"https://assets-eu.researchsquare.com/files/rs-3859914/v1/71dc38c5cf6962190ffe1751.png"},{"id":49950988,"identity":"a8c03cf9-0052-4e04-886f-269436d55c1e","added_by":"auto","created_at":"2024-01-22 06:18:08","extension":"png","order_by":8,"title":"Figure 8","display":"","copyAsset":false,"role":"figure","size":35246,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eAT-TTUs are a novel mechanism for the emergence of STRs. \u003c/strong\u003eFor simplicity, only the alleles involved in the process of STR emergence are depicted. Models of the birth and maturation of (TTA)3 STRs in C184 \u003cstrong\u003eA \u003c/strong\u003eand\u003cstrong\u003e B\u003c/strong\u003e, (ATA)3 STRs in C457 \u003cstrong\u003eC\u003c/strong\u003e, \u003cstrong\u003eD\u003c/strong\u003e,\u003cstrong\u003e \u003c/strong\u003eand\u003cstrong\u003eE\u003c/strong\u003e, and (ATA)3 STRs in C190 \u003cstrong\u003eC \u003c/strong\u003eand\u003cstrong\u003e D\u003c/strong\u003e.\u003c/p\u003e","description":"","filename":"F8.png","url":"https://assets-eu.researchsquare.com/files/rs-3859914/v1/f8610ac43ca959ec578d2105.png"},{"id":52003769,"identity":"d1c70a18-603d-4824-88da-1aa4e54c0ed9","added_by":"auto","created_at":"2024-03-05 08:32:33","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2428566,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3859914/v1/c69993b7-c4c9-4b97-9cf0-0edb62bdf3a8.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Crossover and recombination hotspots massively spread across human genome","fulltext":[{"header":"Introduction","content":"\u003cp\u003eCrossover and recombination, alongside mutation, generate the raw material of evolution and speciation \u003csup\u003e\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e,\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e\u003c/sup\u003e. Recombination hotspots are regions in a genome that exhibit elevated rates of recombination relative to a neutral expectation. Studies on recombination hotspots are mainly founded on mapping crossover events through pedigree analysis and linkage disequilibrium \u003csup\u003e\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e,\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e\u003c/sup\u003e. Identification of those hotspots paved the way for the discovery of PRDM9, a trimethyl transferase, which is associated with hotspot activity in both humans and mouse \u003csup\u003e\u003cspan additionalcitationids=\"CR6\" citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e\u003c/sup\u003e. Using HapMap data, Myers et al. identified a 13-bp \u0026ldquo;core\u0026rdquo; motif \u0026ldquo;CCTCCCTNNCCAC\u0026rdquo; for PRDM9 binding, which is strongly correlated with hotspot activity when it occurs in both repeat and nonrepeat DNA. A close match to this motif was reported to occur in about 40% of the cross-over hotspots known to date \u003csup\u003e\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e\u003c/sup\u003e, and degenerate versions of the motif, of variable binding activity for PRDM9, have been identified in the human genome on centimorgan (cM) scales \u003csup\u003e\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e,\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e\u003c/sup\u003e. The 13-mer motif is the most characterized hotspot locus in human to date. However, the level of expression of PRDM9 should control for only the fraction of targets that are hotspots and the overall temperature of the genome \u003csup\u003e\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eOther indirect approaches, such as phylogenetic and integrated genetic versus physical map analyses performed by several groups have led to the idea that the local rates of recombination are positively correlated with GC content in the human genome \u003csup\u003e\u003cspan additionalcitationids=\"CR13 CR14\" citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e\u003c/sup\u003e and a few other mammals \u003csup\u003e\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e\u003c/sup\u003e. Lined with the above, there are reports that meiotic recombination favors GC-rich alleles over AT-rich alleles, and facilitates local GC-content \u003csup\u003e\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e,\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e\u003c/sup\u003e. When a meiotic recombination hotspot from a GC-rich isochore was inserted into an AT-rich isochore domain, the site adopted the lower recombination activity, characteristic of its new environment \u003csup\u003e\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e\u003c/sup\u003e. It is reported that programmed \u003cem\u003ein vitro\u003c/em\u003e double strand break formation and loading of axial structure proteins are much more prominent in GC-rich isochores \u003csup\u003e\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e,\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e,\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eWe previously reported that CG-rich trinucleotide two-repeat units (CG-TTUs) form colonies of exceeding significance across the human genome, based on Poisson distribution \u003csup\u003e\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e,\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e\u003c/sup\u003e. Several of the large and medium size colonies that were further analyzed in other species, unveiled crossover and recombination hotspots, shared across primates, and in some instances, even in mouse.\u003c/p\u003e \u003cp\u003eHere, we investigated AT-rich trinucleotide two-repeat units (AT-TTUs) with a similar protocol, and discovered that the colonies formed by AT-TTUs were significantly more abundant and larger than the colonies formed by CG-TTUs. These findings challenge the previous findings of bias towards CG-rich sequences at the recombination hotspots. They also challenge the notion that hotspot loci are rarely (if at all) shared between human and closely related species \u003csup\u003e\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e,\u003cspan additionalcitationids=\"CR23 CR24\" citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e\u003c/sup\u003e. These novel crossover sites vastly spread across primate genomes, and are there to greatly enhance the resolution of crossover and recombination hotspots at the molecular level.\u003c/p\u003e"},{"header":"Results","content":"\u003cp\u003e \u003cb\u003eThe majority of the AT-TTUs resided in colonies.\u003c/b\u003e \u003c/p\u003e \u003cp\u003eIn total, 10,330,879 AT-TTUs were detected genome-wide, of which the majority (9,936,861) (96.18%) were arranged in 1,390,055 colonies (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). The AT-TTUs were spread across all chromosomes (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003cb\u003eAT-TTU colonies were significantly more abundant and larger than the CG-TTU colonies.\u003c/b\u003e \u003c/p\u003e \u003cp\u003eIn comparison with the CG-TTU colonies\u003c/p\u003e \u003cp\u003e(\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://figshare.com/articles/dataset/All_possible_CGrich_trinucleotides/23260562\u003c/span\u003e\u003cspan address=\"https://figshare.com/articles/dataset/All_possible_CGrich_trinucleotides/23260562\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e), the\u003c/p\u003e \u003cp\u003ecolonies formed by AT-TTUs were significantly more abundant (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). Large intervals\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eof chromosomes were occupied by colony intervals in many chromosomes, for example\u003c/p\u003e \u003cp\u003ein chromosome 4. Furthermore, the pattern of distribution of the AT-TTU colonies across\u003c/p\u003e \u003cp\u003ehuman chromosomes was significantly different from the CG-TTU colonies. For example,\u003c/p\u003e \u003cp\u003ewhereas chromosome 1 had the highest percentage of CG-TTU colonies \u003csup\u003e\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e\u003c/sup\u003e, AT-TTU\u003c/p\u003e \u003cp\u003ecolonies reached highest percentage on chromosome 4.\u003c/p\u003e \u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eSeveral of the large and medium-size AT-TTU colonies coincided with extensive dynamicity in great apes\u003c/h2\u003e \u003cp\u003eSeveral of the large and medium-size AT-TTU colonies in human were also detected in other great apes (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Exceedingly dynamic events were detected across those colonies, affecting the AT-TTUs and the flanking sequences to those units. Across the colonies, the AT-TTUs were either pure or overlaps of two or more pure units.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eSeveral large and medium-size AT-TTU colonies in human and their corresponding colonies in other primates.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"8\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c8\" colnum=\"8\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colspan=\"5\" nameend=\"c5\" namest=\"c1\"\u003e \u003cp\u003eColony Formula\u003csup\u003eb\u003c/sup\u003e\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eChr.\u003c/p\u003e \u003cp\u003eNo.\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eLocation\u003c/p\u003e \u003cp\u003e(Colony interval)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c8\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eλ value\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eColony Size\u003c/p\u003e \u003cp\u003ein Human\u003csup\u003ea\u003c/sup\u003e\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHuman\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eChimpanzee\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eGorilla\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eMacaque\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC718\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e[(ATT)2]32\u003c/p\u003e \u003cp\u003e[(ATA)2]5\u003c/p\u003e \u003cp\u003e[(AAT)2]11\u003c/p\u003e \u003cp\u003e[(TAA)2]2\u003c/p\u003e \u003cp\u003e[(TTA)2]318\u003c/p\u003e \u003cp\u003e[(TAT)2]350\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e[(ATT)2]21\u003c/p\u003e \u003cp\u003e[(ATA)2]5\u003c/p\u003e \u003cp\u003e[(AAT)2]3\u003c/p\u003e \u003cp\u003e[(TAA)2]2\u003c/p\u003e \u003cp\u003e[(TTA)2]262\u003c/p\u003e \u003cp\u003e[(TAT)2]288\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e[(ATT)2]3\u003c/p\u003e \u003cp\u003e[(ATA)2]2\u003c/p\u003e \u003cp\u003e[(TAA)2]1\u003c/p\u003e \u003cp\u003e[(TTA)2]4\u003c/p\u003e \u003cp\u003e[(TAT)2]7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e11\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e11:114603789\u0026ndash;114625648\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e75.27\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC457\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e[(ATT)2]13\u003c/p\u003e \u003cp\u003e[(ATA)2]160\u003c/p\u003e \u003cp\u003e[(AAT)2]40\u003c/p\u003e \u003cp\u003e[(TAA)2]43\u003c/p\u003e \u003cp\u003e[(TTA)2]8\u003c/p\u003e \u003cp\u003e[(TAT)2]193\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e22\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e22:18728881\u0026ndash;18733753\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e16.78\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC350\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e[(ATT)2]12\u003c/p\u003e \u003cp\u003e[(ATA)2]165\u003c/p\u003e \u003cp\u003e[(AAT)2]15\u003c/p\u003e \u003cp\u003e[(TAA)2]11\u003c/p\u003e \u003cp\u003e[(TTA)2]11\u003c/p\u003e \u003cp\u003e[(TAT)2]136\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e11\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e11:96561723\u0026ndash;96568076\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e21.88\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC317\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e[(ATT)2]115\u003c/p\u003e \u003cp\u003e[(ATA)2]59\u003c/p\u003e \u003cp\u003e[(AAT)2]8\u003c/p\u003e \u003cp\u003e[(TAA)2]4\u003c/p\u003e \u003cp\u003e[(TTA)2]14\u003c/p\u003e \u003cp\u003e[(TAT)2]117\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e[(ATT)2]102\u003c/p\u003e \u003cp\u003e[(ATA)2]47\u003c/p\u003e \u003cp\u003e[(AAT)2]5\u003c/p\u003e \u003cp\u003e[(TAA)2]3\u003c/p\u003e \u003cp\u003e[(TTA)2]12\u003c/p\u003e \u003cp\u003e[(TAT)2]103\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e12\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e12:79456025\u0026ndash;79468112\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e41.62\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC287\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e[(ATT)2]11\u003c/p\u003e \u003cp\u003e[(ATA)2]112\u003c/p\u003e \u003cp\u003e[(AAT)2]30\u003c/p\u003e \u003cp\u003e[(TAA)2]13\u003c/p\u003e \u003cp\u003e[(TTA)2]16\u003c/p\u003e \u003cp\u003e[(TAT)2]105\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e[(ATT)2]2\u003c/p\u003e \u003cp\u003e[(ATA)2]17\u003c/p\u003e \u003cp\u003e[(AAT)2]1\u003c/p\u003e \u003cp\u003e[(TAA)2]1\u003c/p\u003e \u003cp\u003e[(TTA)2]2\u003c/p\u003e \u003cp\u003e[(TAT)2]24\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e[(ATT)2]2\u003c/p\u003e \u003cp\u003e[(ATA)2]3\u003c/p\u003e \u003cp\u003e[(AAT)2]2\u003c/p\u003e \u003cp\u003e[(TAA)2]1\u003c/p\u003e \u003cp\u003e[(TTA)2]2\u003c/p\u003e \u003cp\u003e[(TAT)2]6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eX\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eX:143653179\u0026ndash;143659751\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e22.63\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC275\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e[(ATT)2]6\u003c/p\u003e \u003cp\u003e[(ATA)2]135\u003c/p\u003e \u003cp\u003e[(AAT)2]13\u003c/p\u003e \u003cp\u003e[(TAA)2]10\u003c/p\u003e \u003cp\u003e[(TTA)2]6\u003c/p\u003e \u003cp\u003e[(TAT)2]105\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e22\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e22:18891229\u0026ndash;18896934\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e19.65\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC267\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e[(ATT)2]4\u003c/p\u003e \u003cp\u003e[(ATA)2]151\u003c/p\u003e \u003cp\u003e[(AAT)2]4\u003c/p\u003e \u003cp\u003e[(TAA)2]4\u003c/p\u003e \u003cp\u003e[(TTA)2]5\u003c/p\u003e \u003cp\u003e[(TAT)2]99\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e2:16146128\u0026ndash;16148756\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e9.05\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC255\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e[(ATA)2]4\u003c/p\u003e \u003cp\u003e[(AAT)2]247\u003c/p\u003e \u003cp\u003e[(TAA)2]2\u003c/p\u003e \u003cp\u003e[(TTA)2]1\u003c/p\u003e \u003cp\u003e[(TAT)2]1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e[(ATA)2]2\u003c/p\u003e \u003cp\u003e[(AAT)2]16\u003c/p\u003e \u003cp\u003e[(TAA)2]1\u003c/p\u003e \u003cp\u003e[(TTA)2]1\u003c/p\u003e \u003cp\u003e[(TAT)2]1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e2:231822812\u0026ndash;231850574\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e95.60\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC212\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e[(ATA)2]101\u003c/p\u003e \u003cp\u003e[(AAT)2]4\u003c/p\u003e \u003cp\u003e[(TAA)2]6\u003c/p\u003e \u003cp\u003e[(TTA)2]2\u003c/p\u003e \u003cp\u003e[(TAT)2]99\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e[(ATT)2]20\u003c/p\u003e \u003cp\u003e[(ATA)2]95\u003c/p\u003e \u003cp\u003e[(AAT)2]20\u003c/p\u003e \u003cp\u003e[(TAA)2]16\u003c/p\u003e \u003cp\u003e[(TTA)2]8\u003c/p\u003e \u003cp\u003e[(TAT)2]88\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e[(ATT)2]1\u003c/p\u003e \u003cp\u003e[(ATA)2]17\u003c/p\u003e \u003cp\u003e[(AAT)2]1\u003c/p\u003e \u003cp\u003e[(TAA)2]3\u003c/p\u003e \u003cp\u003e[(TTA)2]1\u003c/p\u003e \u003cp\u003e[(TAT)2]20\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eX\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eX: 108772450\u0026ndash;108776693\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e14.61\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC200\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e[(ATT)2]4\u003c/p\u003e \u003cp\u003e[(ATA)2]77\u003c/p\u003e \u003cp\u003e[(AAT)2]76\u003c/p\u003e \u003cp\u003e[(TAA)2]9\u003c/p\u003e \u003cp\u003e[(TTA)2]2\u003c/p\u003e \u003cp\u003e[(TAT)2]32\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e[(ATT)2]2\u003c/p\u003e \u003cp\u003e[(ATA)2]72\u003c/p\u003e \u003cp\u003e[(AAT)2]70\u003c/p\u003e \u003cp\u003e[(TAA)2]7\u003c/p\u003e \u003cp\u003e[(TTA)2]2\u003c/p\u003e \u003cp\u003e[(TAT)2]30\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e[(ATA)2]80\u003c/p\u003e \u003cp\u003e[(AAT)2]78\u003c/p\u003e \u003cp\u003e[(TAA)2]10\u003c/p\u003e \u003cp\u003e[(TTA)2]3\u003c/p\u003e \u003cp\u003e[(TAT)2]29\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e7:37785667\u0026ndash;37794029\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e28.80\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC198\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e[(ATT)2]9\u003c/p\u003e \u003cp\u003e[(ATA)2]62\u003c/p\u003e \u003cp\u003e[(AAT)2]14\u003c/p\u003e \u003cp\u003e[(TAA)2]15\u003c/p\u003e \u003cp\u003e[(TTA)2]5\u003c/p\u003e \u003cp\u003e[(TAT)2]93\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e22\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e22:18235269\u0026ndash;18238724\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e11.90\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC195\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e[(ATT)2]12\u003c/p\u003e \u003cp\u003e[(ATA)2]61\u003c/p\u003e \u003cp\u003e[(AAT)2]9\u003c/p\u003e \u003cp\u003e[(TAA)2]6\u003c/p\u003e \u003cp\u003e[(TTA)2]15\u003c/p\u003e \u003cp\u003e[(TAT)2]92\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e[(ATT)2]10\u003c/p\u003e \u003cp\u003e[(ATA)2]48\u003c/p\u003e \u003cp\u003e[(AAT)2]3\u003c/p\u003e \u003cp\u003e[(TAA)2]4\u003c/p\u003e \u003cp\u003e[(TTA)2]10\u003c/p\u003e \u003cp\u003e[(TAT)2]58\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e[(ATT)2]6\u003c/p\u003e \u003cp\u003e[(ATA)2]31\u003c/p\u003e \u003cp\u003e[(AAT)2]4\u003c/p\u003e \u003cp\u003e[(TAA)2]4\u003c/p\u003e \u003cp\u003e[(TTA)2]4\u003c/p\u003e \u003cp\u003e[(TAT)2]17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e10:67724852\u0026ndash;67731164\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e21.74\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC190\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e[(ATT)2]2\u003c/p\u003e \u003cp\u003e[(ATA)2]38\u003c/p\u003e \u003cp\u003e[(AAT)2]5\u003c/p\u003e \u003cp\u003e[(TAA)2]6\u003c/p\u003e \u003cp\u003e[(TTA)2]3\u003c/p\u003e \u003cp\u003e[(TAT)2]136\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e2:194462444\u0026ndash;194465074\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e9.06\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC184\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e[(ATT)2]34\u003c/p\u003e \u003cp\u003e[(ATA)2]18\u003c/p\u003e \u003cp\u003e[(AAT)2]30\u003c/p\u003e \u003cp\u003e[(TAA)2]4\u003c/p\u003e \u003cp\u003e[(TTA)2]61\u003c/p\u003e \u003cp\u003e[(TAT)2]37\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e[(ATT)2]23\u003c/p\u003e \u003cp\u003e[(ATA)2]10\u003c/p\u003e \u003cp\u003e[(AAT)2]19\u003c/p\u003e \u003cp\u003e[(TAA)2]3\u003c/p\u003e \u003cp\u003e[(TTA)2]34\u003c/p\u003e \u003cp\u003e[(TAT)2]24\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e[(ATT)2]19\u003c/p\u003e \u003cp\u003e[(ATA)2]10\u003c/p\u003e \u003cp\u003e[(AAT)2]17\u003c/p\u003e \u003cp\u003e[(TAA)2]2\u003c/p\u003e \u003cp\u003e[(TTA)2]26\u003c/p\u003e \u003cp\u003e[(TAT)2]19\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e[(ATT)2]6\u003c/p\u003e \u003cp\u003e[(ATA)2]1\u003c/p\u003e \u003cp\u003e[(AAT)2]3\u003c/p\u003e \u003cp\u003e[(TAA)2]1\u003c/p\u003e \u003cp\u003e[(TTA)2]2\u003c/p\u003e \u003cp\u003e[(TAT)2]5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e6:77601972\u0026ndash;77604184\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e7.62\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC182\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e[(ATT)2]13\u003c/p\u003e \u003cp\u003e[(ATA)2]51\u003c/p\u003e \u003cp\u003e[(AAT)2]17\u003c/p\u003e \u003cp\u003e[(TAA)2]16\u003c/p\u003e \u003cp\u003e[(TTA)2]12\u003c/p\u003e \u003cp\u003e[(TAT)2]73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e[(ATT)2]6\u003c/p\u003e \u003cp\u003e[(ATA)2]65\u003c/p\u003e \u003cp\u003e[(AAT)2]12\u003c/p\u003e \u003cp\u003e[(TAA)2]11\u003c/p\u003e \u003cp\u003e[(TTA)2]9\u003c/p\u003e \u003cp\u003e[(TAT)2]38\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e[(ATT)2]4\u003c/p\u003e \u003cp\u003e[(ATA)2]31\u003c/p\u003e \u003cp\u003e[(AAT)2]2\u003c/p\u003e \u003cp\u003e[(TAA)2]2\u003c/p\u003e \u003cp\u003e[(TTA)2]6\u003c/p\u003e \u003cp\u003e[(TAT)2]22\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e[(ATT)2]3\u003c/p\u003e \u003cp\u003e[(ATA)2]11\u003c/p\u003e \u003cp\u003e[(AAT)2]2\u003c/p\u003e \u003cp\u003e[(TAA)2]3\u003c/p\u003e \u003cp\u003e[(TTA)2]7\u003c/p\u003e \u003cp\u003e[(TAT)2]15\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e14\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e14:52527096\u0026ndash;52531874\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e16.45\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC175\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e[(ATT)2]5\u003c/p\u003e \u003cp\u003e[(ATA)2]68\u003c/p\u003e \u003cp\u003e[(AAT)2]5\u003c/p\u003e \u003cp\u003e[(TAA)2]7\u003c/p\u003e \u003cp\u003e[(TTA)2]23\u003c/p\u003e \u003cp\u003e[(TAT)2]67\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e7:54395223\u0026ndash;54397576\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e8.10\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC173\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e[(ATA)2]69\u003c/p\u003e \u003cp\u003e[(AAT)2]64\u003c/p\u003e \u003cp\u003e[(TAA)2]18\u003c/p\u003e \u003cp\u003e[(TAT)2]22\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e16:18565943\u0026ndash;18570325\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e15.09\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC161\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e[(ATT)2]68\u003c/p\u003e \u003cp\u003e[(ATA)2]17\u003c/p\u003e \u003cp\u003e[(AAT)2]2\u003c/p\u003e \u003cp\u003e[(TAA)2]2\u003c/p\u003e \u003cp\u003e[(TTA)2]8\u003c/p\u003e \u003cp\u003e[(TAT)2]64\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e[(ATT)2]65\u003c/p\u003e \u003cp\u003e[(ATA)2]17\u003c/p\u003e \u003cp\u003e[(AAT)2]2\u003c/p\u003e \u003cp\u003e[(TAA)2]2\u003c/p\u003e \u003cp\u003e[(TTA)2]8\u003c/p\u003e \u003cp\u003e[(TAT)2]64\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e[(ATT)2]68\u003c/p\u003e \u003cp\u003e[(ATA)2]17\u003c/p\u003e \u003cp\u003e[(AAT)2]3\u003c/p\u003e \u003cp\u003e[(TAA)2]2\u003c/p\u003e \u003cp\u003e[(TTA)2]4\u003c/p\u003e \u003cp\u003e[(TAT)2]65\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e3:8693642\u0026ndash;8702099\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e29.12\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003ctfoot\u003e \u003ctr\u003e\u003ctd colspan=\"8\"\u003e\u003csup\u003ea\u003c/sup\u003eColony size, chromosomal location, colony interval, and \u003cb\u003eλ value\u003c/b\u003e are based on the human genome, as reference. The corresponding colonies in other species were identified, using BLASTN. Instances in which the colonies were partially or not sequenced (such as C287, C212, and C200 in gorilla), or lacked the corresponding colony in a species were left blank. Poisson probability values for all the colony sizes in this table is inherent zero. None of the colonies in this table were detected in mouse lemur or mouse.\u003c/td\u003e\u003c/tr\u003e \u003ctr\u003e\u003ctd colspan=\"8\"\u003e\u003csup\u003eb\u003c/sup\u003eFormulas represent absolute numbers of units, regardless of being pure or overlapping.\u003c/td\u003e\u003c/tr\u003e \u003c/tfoot\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eThe largest AT-TTU colony in human was a compound colony of 718 units (C718), located on chromosome 11, which was detected with exceeding dynamicity in human and chimpanzee, and at a far lesser extent in gorilla. This colony reached maximum complexity and size in human (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eThe absolute number of the AT-TTUs and the distribution of the units in the pure and overlapping compartments were exceedingly dynamic across those species, adding multiple layers of complexity of the events, and leading to massively divergent compositions. Most of the units in C718 and its orthologous colonies were in the overlapping compartment (Figs.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e and \u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eA).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eFurthermore, the immediate flanking sequences of the units were significantly dynamic with respect to mutations (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eB).\u003c/p\u003e \u003cp\u003e \u003cb\u003eModels proposed for the evolution of pure and overlapping units.\u003c/b\u003e \u003c/p\u003e \u003cp\u003eSome of the pure units were the inverted or palindromic sequences of one another, and probably emerged, and resulted in DNA breakage and recombination events inherent to inverted and palindromic sequences, for example, two pure units of TTATTA and ATTATT (inversion), and TTATTA and TAATAA (palindrome).\u003c/p\u003e \u003cp\u003eOverlapping units were a consequence of unequal crossovers among the pure units. For example, in C718, the most prevalent overlapping unit, TTATTAT, was the consequence of unequal crossovers between pure units, TTATTA and TATTAT (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eA). In another example in C718, the overlapping unit, AATAATTATTAT, was the consequence of several unequal crossovers across units (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eA). It is conceivable that reverse processes leading to the overlapping units could result in the re-emergence of the pure units.\u003c/p\u003e \u003cp\u003eThe flanking sequences of the units were also highly dynamic (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eB), signifying the occurrence of crossovers at the sites of the AT-TTUs, and coupled breakage and repair at, and around these sites.\u003c/p\u003e \u003cp\u003e \u003cstrong\u003eCoi\u003c/strong\u003e \u003cp\u003e \u003cb\u003encidence of some of the colonies beyond great apes.\u003c/b\u003e \u003c/p\u003e \u003c/p\u003e \u003cp\u003eSeveral colonies, such as C212, C200, and C184 coincided beyond great apes, and included macaque (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). As an example, in C184, the colonies were shared dynamically in human, chimpanzee, gorilla, and macaque, and there was a directional incremented trend of complexity of the events and units in human (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e). Pure and overlapping units were also detected across this colony in human and other primates. For example, TATTATTA, was the consequence of unequal crossovers between TATTAT, ATTATT, and TTATTA pure units.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003cb\u003eColonies that were detected in human and not the other five species studied.\u003c/b\u003e \u003c/p\u003e \u003cp\u003eWe also detected colonies that were found in human only (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e), such as C457 (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003eA) and C190 (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003eB).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003ewe detected strings of consecutive pure units recombining with each other, or pure and overlapping units recombining with each other.\u003c/p\u003e \u003cp\u003e \u003cb\u003eAT-TTUs are a mechanism for the emergence of AT short tandem repeats (STRs).\u003c/b\u003e \u003c/p\u003e \u003cp\u003eThe AT-TTUs and coupled unequal crossovers and recombination at these sites result in the emergence of STRs (repeats of \u0026ge;\u0026thinsp;3). For example, in C184, the (TTA)3 STR could be a consequence of unequal crossovers through various paths (Fig.\u0026nbsp;\u003cspan refid=\"Fig8\" class=\"InternalRef\"\u003e8\u003c/span\u003eA and B). In other examples, in C457 and C190, unequal crossovers gave rise to overlapping units for the emergence of several (ATA)3 STRs (Fig.\u0026nbsp;\u003cspan refid=\"Fig8\" class=\"InternalRef\"\u003e8\u003c/span\u003eC,D, and E). We detected the pure units and intermediate overlapping units necessary for the emergence of STRs in the same (or orthologous) colonies that the STRs were detected.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e"},{"header":"Discussion","content":"\u003cp\u003eThe bulk of literature is dominated by reports of the preference of CG- over AT-rich sequences at the recombination hotspots \u003csup\u003e\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e,\u003cspan additionalcitationids=\"CR27 CR28 CR29 CR30\" citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e\u003c/sup\u003e. Limited reports of the involvement of AT-rich sequences in recombination and consequent translocations are available in the literature, which primarily concern AT-rich palindromic or inverted sequences. Those events are mainly involved in chromosomal translocations and deletions, for example in chromosomes 11, 17, and 22 \u003csup\u003e32\u0026ndash;34\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eHere, we report a phenomenon, in which AT-TTUs colonize across the genome with exceedingly significant Poisson probability values. In fact, the majority of AT-TTUs in the human genome reside in colonies, and those colonies span significant intervals of several chromosomes. The AT-TTU colonies were significantly larger and more complex than the CG-rich colonies that we reported previously \u003csup\u003e\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e,\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e\u003c/sup\u003e. These findings support a more significant role of AT-rich sequences in comparison with CG-rich sequences, as crossover and recombination hotspots. While the AT-TTU crossover hotspots were ubiquitous, the most refined maps of recombination identified so far are on the scales of cM \u003csup\u003e\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e,\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eThe presence of pure units and overlapping units of those pure units, and the fact that the common elements across the colonies were the AT-TTUs, signify that the main reason for the hotspot events in those colonies is the AT-TTUs, and not their flanking sequences. The inversions and palindromes as a result of the pure and overlapping units increase the rate of various genetic rearrangement events and recombination across the colonies. Palindromes and inversions are known to be recombinogenic in the genomes, and a risk to instability \u003csup\u003e\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e,\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eThe flanking sequences of the AT-TTUs were also extensively dynamic. The very high dynamicity of the flanking sequences was in line with the previous reports that flanking sequences to the recombination sites are prone to mutations \u003csup\u003e\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e,\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eSome of the identified colonies, which were further studied in other primates, were shared in those primates with exceeding dynamicity of the events. These findings challenge the long-lasting literature on the rarity of shared recombination hotspots between human and closely related species \u003csup\u003e\u003cspan additionalcitationids=\"CR23 CR24\" citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e\u003c/sup\u003e. An isolate report of shared hotspot loci between human and chimpanzee was at β-globin and HLA regions on chromosome 21, which was based on high Bayes factors of shared hotspots at locations within both regions\u003csup\u003e\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e\u003c/sup\u003e. Our data extend crossover and recombination hotspot sharedness across primates, and envision a new perspective in the field, with respect to mechanistic, evolutionary, and magnitude of crossovers and recombination.\u003c/p\u003e \u003cp\u003eIt is reasonable to consider the AT-TTUs a novel genomic entity, as although they are repeats, they do not conform to the conventional definition of repetitive DNA sequences, such as microsatellites and minisatellites \u003csup\u003e\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e\u003c/sup\u003e. Neither the well-characterized recombination hotspot 13-mer, nor the degenerate sequences of this sequence could explain the identified colonies and the extent of the events occurring across those colonies.\u003c/p\u003e \u003cp\u003eIn comparison with CG-TTU colonies, the AT-TTU colonies (at least the colonies that were further analyzed in additional primates), were mainly more complex in human, at a directional trend. Furthermore, the rate of detecting those colonies in human only (in comparison with the other species that were studied) was higher than the CG-TTU colonies\u003csup\u003e\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e\u003c/sup\u003e. One explanation may be that the mechanisms involved in the AT-TTU colonies have evolved more recently than the CG-TTU colonies. This is also supported by the fact that we could not identify AT-TTU orthologous colonies in mouse lemur and mouse, whereas in the instance of CG-TTU colonies, several of the colonies were identified in those species \u003csup\u003e\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eThe AT-TTUs and the crossovers coupled with those units are a novel mechanism for the emergence of STRs. This follows from our observations that all the pure and intermediate overlapping units necessary for the birth and maturation of a given STR were detectable in the same (or orthologous) colonies. The evolutionary, biological, and pathological implications of STRs are an emerging topic of research among others \u003csup\u003e\u003cspan additionalcitationids=\"CR43 CR44\" citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eIn summary, in view of the events and mechanisms associated with the identified units, their abundance and ubiquity throughout the genomes studied, and their exceedingly significant colonization based on Poisson distribution, we predict these units of phenomenal evolutionary and biological consequences. However, this is the tip of the iceberg, and the evolutionary purpose of this phenomenon is yet to be discovered in the future studies.\u003c/p\u003e"},{"header":"Conclusion","content":"\u003cp\u003eIn conclusion, our findings unveil massive AT-TTUs as crossover and recombination hotspots in human and several other primates. These findings challenge the hypothesis that CG-rich sequences are preferred over AT-rich sequences at the crossover and recombination hotspots. Our findings also unveil sharedness of these hotspots, at least across great apes and Old-World monkeys, and challenge once again, the hypothesis that human and closely related species do not share recombination hotspots. AT-TTUs are a novel mechanism for the emergence of STRs across species. We propose that, with respect to crossovers and recombination, genomes of primates are far more dynamic than previously imagined.\u003c/p\u003e"},{"header":"Methods","content":"\u003cp\u003e \u003cb\u003eWhole-genome extraction of AT-TTUs in human.\u003c/b\u003e \u003c/p\u003e \u003cp\u003eA Java software package was created (available at \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://github.com/arabfard/Java_STR_Finder\u003c/span\u003e\u003cspan address=\"https://github.com/arabfard/Java_STR_Finder\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) to facilitate the extraction of specific type of DNA sequence units, known as AT-TTUs, including AATAAT, ATAATA, ATTATT, TTATTA, TATTAT, and TAATAA, along with their corresponding locations. To ensure the accuracy and reliability of the data obtained from the algorithm, a validation process was conducted. This involved randomly examining these units across the entire genome. By manually inspecting the identified units, we were able to detect any potential errors or false positives generated by the algorithm. Through this verification process, we confirmed that the algorithm functioned as intended, and produced reliable results. In order to extract all AT-TTUs, we utilized the latest version of the human genome assembly (GRCh38. p14) obtained from the UCSC genome browser (accessible at \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://hgdownload.soe.ucsc.edu\u003c/span\u003e\u003cspan address=\"https://hgdownload.soe.ucsc.edu\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003cb\u003eComparison of the AT-TTU versus CG-TTU colonies in the human genome.\u003c/b\u003e \u003c/p\u003e \u003cp\u003eThe AT-TTU colonies from the present study were compared with the CG-TTU colonies,\u003c/p\u003e \u003cp\u003eyielded from our previous study \u003csup\u003e\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e\u003c/sup\u003e,\u003c/p\u003e \u003cp\u003e \u003cspan class=\"ExternalRef\"\u003e \u003cspan class=\"RefSource\"\u003ehttps://figshare.com/articles/dataset/All_possible_CG-rich_trinucleotides/23260562\u003c/span\u003e \u003cspan address=\"https://figshare.com/articles/dataset/All_possible_CG-rich_trinucleotides/23260562\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e \u003c/span\u003e.\u003c/p\u003e\n\u003ch3\u003eThe extraction algorithm\u003c/h3\u003e\n\u003cp\u003eThe developed Java program was used to extract all possible AT-TTUs, as follows: AATAAT, ATAATA, ATTATT, TTATTA, TATTAT, and TAATAA, from the human genome sequence. The program initiated its search from the first nucleotide of the genome, continuously scanning for duplicated occurrences of AT-rich trinucleotide cores. It employed a window frame consisting of 6 nucleotides to identify instances of the core sequence repeating twice. Upon discovering a unit, the program recorded the number and location of the two-repeat occurrences. It then proceeded to search for new AT-TTUs, starting from the next nucleotide.\u003c/p\u003e \u003cp\u003eTo validate the results, the final list of identified AT-TTUs underwent manual evaluation, using the Ensembl genome browser 109 (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://asia.ensembl.org/index.html\u003c/span\u003e\u003cspan address=\"https://asia.ensembl.org/index.html\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e). The precise locations of the AT-TTUs were determined as follows: The output was organized and classified in an Excel file, where the start and end points of each unit were determined within the genome. By subtracting the start and end points of subsequent units, colonies were identified. If the resulting distance was less than 500 bp, the units were considered part of the same colony. Subsequently, a list of colonies consisting of two or more units was compiled, the total count of colonies was determined, and the output was saved in a readily available format (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.6084/m9.figshare.24202461.v1\u003c/span\u003e\u003cspan address=\"10.6084/m9.figshare.24202461.v1\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e).\u003c/p\u003e \u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003eScreening several of the large and medium-size human colonies in other species\u003c/h2\u003e \u003cp\u003eThe Ensembl Genome Browser 109 was utilized to conduct a comparative analysis of various size colonies in human and several other species, including chimpanzee, gorilla, macaque, mouse lemur, and mouse (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). The analysis involved employing the BLASTN program available on the Ensembl Genome Browser 109 (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://asia.ensembl.org/index.html\u003c/span\u003e\u003cspan address=\"https://asia.ensembl.org/index.html\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e).\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec9\" class=\"Section2\"\u003e \u003ch2\u003eStatistical analysis\u003c/h2\u003e \u003cp\u003eTo assess the significance of differences between two frequency groups, the Wilcoxon Signed-Rank Test was employed. We utilized the Poisson distribution to determine the λ value and probability distribution of various size colonies (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). The Poisson distribution is commonly used to model the occurrence of rare events within a given interval. In our study, we applied this distribution to model the occurrence of AT-TTUs of all possible AT-rich trinucleotide units in the human genome. This modeling considers the average number of units in an interval, which is proportional to the interval's length.\u003c/p\u003e \u003cp\u003eThe Poisson process assumes that the occurrence of these units is random and independent of each other. Furthermore, it assumes that their distribution across the genome is relatively uniform.\u003c/p\u003e \u003cp\u003eIn order to calculate the probability of units in the colony occurrence, using the Poisson density function, we needed to determine the expected number of units per colony interval of the genome. This involved dividing the total number of identified colonies by the total length of the genome and applying a correction factor to account for the expected number of colonies. By applying the Poisson distribution, we were able to calculate the probability of the number of different units, occurring in a given colony. This calculation was performed, using the Poisson density function, with specific parameters that capture the characteristics of the distribution and the expected rate of unit occurrence in the colony.\u003cdiv id=\"Equa\" class=\"Equation\"\u003e\u003cdiv format=\"TEX\" class=\"mathdisplay\" id=\"FileID_Equa\" name=\"EquationSource\"\u003e\n$${\\lambda }=\\frac{Colony Interval \\text{*}\\text{a}\\text{l}\\text{l} \\text{p}\\text{o}\\text{s}\\text{s}\\text{i}\\text{b}\\text{l}\\text{e} \\text{u}\\text{n}\\text{i}\\text{t}\\text{s} \\text{o}\\text{f} \\text{A}\\text{T}-\\text{r}\\text{i}\\text{c}\\text{h} \\text{t}\\text{r}\\text{i}\\text{n}\\text{u}\\text{c}\\text{l}\\text{e}\\text{o}\\text{t}\\text{i}\\text{d}\\text{e}\\text{s} \\text{i}\\text{n} \\text{t}\\text{h}\\text{e} \\text{g}\\text{e}\\text{n}\\text{o}\\text{m}\\text{e} }{3000000000\\left(3\\text{g}\\text{b}\\right)}$$\u003c/div\u003e\u003c/div\u003e\u003c/p\u003e \u003cp\u003eFor example, the largest colony, C718, spanned 21,859 bases. On the other hand, the total number of AT-TTUs in the human genome was about 10,330,879, resulting in λ\u0026thinsp;=\u0026thinsp;75.27 for the C718 colony, meaning that based on the Poisson distribution, the average expected count of AT-TTUs in the 21,859 interval was 75.27. Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e presents values of λ for several colony sizes, the calculated probability of all of which was inherent zero.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec10\" class=\"Section2\"\u003e \u003ch2\u003eVisualization\u003c/h2\u003e \u003cp style='margin-top:0cm;margin-right:0cm;margin-bottom:8.0pt;margin-left:0cm;font-size:11.0pt;font-family:\"Calibri\",sans-serif;line-height:200%;'\u003e\u003cspan style='font-size:16px;line-height:200%;font-family:\"Arial\",sans-serif;'\u003eThe six pure AT-TTUs were visualized as:\u0026nbsp;\u003c/span\u003e\u003cstrong\u003e\u003cspan style='font-size:19px;line-height:200%;font-family:\"Courier New\";color:black;background:red;'\u003eTTATTA\u003c/span\u003e\u003c/strong\u003e\u003cspan style='font-size:16px;line-height:200%;font-family:\"Arial\",sans-serif;'\u003e,\u0026nbsp;\u003c/span\u003e\u003cstrong\u003e\u003cspan style='font-size:19px;line-height:200%;font-family:\"Courier New\";color:black;background:fuchsia;'\u003eTATTAT\u003c/span\u003e\u003c/strong\u003e\u003cspan style='font-size:16px;line-height:200%;font-family:\"Arial\",sans-serif;'\u003e,\u0026nbsp;\u003c/span\u003e\u003cstrong\u003e\u003cspan style='font-size:19px;line-height:200%;font-family:\"Courier New\";color:black;background:lime;'\u003eAATAAT\u003c/span\u003e\u003c/strong\u003e\u003cspan style='font-size:16px;line-height:200%;font-family:\"Arial\",sans-serif;'\u003e,\u0026nbsp;\u003c/span\u003e\u003cstrong\u003e\u003cspan style='font-size:19px;line-height:200%;font-family:\"Courier New\";color:black;background:yellow;'\u003eATTATT\u003c/span\u003e\u003c/strong\u003e\u003cspan style='font-size:16px;line-height:200%;font-family:\"Arial\",sans-serif;'\u003e,\u003c/span\u003e\u003cstrong\u003e\u003cspan style='font-size:19px;line-height:200%;font-family:\"Courier New\";color:black;'\u003e\u0026nbsp;\u003c/span\u003e\u003c/strong\u003e\u003cstrong\u003e\u003cspan style='font-size:19px;line-height:200%;font-family:\"Courier New\";color:black;background:aqua;'\u003eATAATA\u003c/span\u003e\u003c/strong\u003e\u003cspan style='font-size:16px;line-height:200%;font-family:\"Arial\",sans-serif;'\u003e, and\u003c/span\u003e\u003cstrong\u003e\u003cspan style='font-size:19px;line-height:200%;font-family:\"Courier New\";color:black;'\u003e\u0026nbsp;\u003cspan style=\"background:darkcyan;\"\u003eTAATAA\u003c/span\u003e\u003c/span\u003e\u003c/strong\u003e\u003cspan style='font-size:16px;line-height:200%;font-family:\"Arial\",sans-serif;'\u003e. \u0026nbsp; The overlapping units were also highlighted, using various highlight and text colors.\u003c/span\u003e\u003c/p\u003e \u003c/div\u003e"},{"header":"Abbreviations","content":"\u003cp\u003eAT-TTU\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;AT-rich Trinucleotide Two-repeat Unit\u003c/p\u003e\n\u003cp\u003eC:\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Colony\u003c/p\u003e\n\u003cp\u003eCG-TTU\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;CG-rich Trinucleotide Two-repeat Unit\u003c/p\u003e\n\u003cp\u003eSTR \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;Short Tandem Repeat\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eEthics approval and consent to participate:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003cp\u003e\u003cbr\u003e\u003cstrong\u003eConsent for publication:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003cp\u003e\u003cbr\u003e\u003cstrong\u003eAcknowledgments:\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding:\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor contributions:\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConceptualization:\u003c/strong\u003e MO\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eMethodology:\u003c/strong\u003e MA\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eInvestigation:\u003c/strong\u003e MA, SKh, SA, SV, HB, NT\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eVisualization:\u003c/strong\u003e MA, SA, SKh\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eProject administration:\u003c/strong\u003e MO, AD, HRKh\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eSupervision:\u003c/strong\u003e MO\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eWriting \u0026ndash; original draft:\u003c/strong\u003e MO, MA\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eWriting \u0026ndash; review \u0026amp; editing:\u003c/strong\u003e MO, MA, HO\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting interests:\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNone to be declared.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData and materials availability:\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eRaw data for AT-TTUs are available at the following link:\u0026nbsp;\u003c/p\u003e\n\u003cp\u003ehttps://figshare.com/articles/dataset/AT-rich_trinucleotides/24202461\u003c/p\u003e\n\u003cp\u003eRaw data for CG-TTUs are available at the following link:\u003c/p\u003e\n\u003cp\u003ehttps://figshare.com/articles/dataset/All_possible_CG-rich_trinucleotides/23260562\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eOrtiz-Barrientos, D., Engelstadter, J. \u0026amp; Rieseberg, L. 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Gene 893, 147968, doi:\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.gene.2023.147968\u003c/span\u003e\u003cspan address=\"10.1016/j.gene.2023.147968\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e (2024).\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Human, AT-rich trinucleotide, Two-repeat, Unequal crossover, Recombination hotspot: Primate, Shared","lastPublishedDoi":"10.21203/rs.3.rs-3859914/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-3859914/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThe recombination landscape and subsequent natural selection have vast consequences in evolution and speciation. However, most of the recombination hotspots in the human genome are yet to be discovered. We previously reported colonies of CG-rich trinucleotide two-repeat units (CG-TTUs) across the human genome, several of which were shared, with extensive dynamicity, as phylogenetically distant as in mouse. Here we performed a whole-genome analysis of AT-rich trinucleotide two-repeat units (AT-TTUs) in human and found that the majority (96%) resided in approximately 1.4\u0026nbsp;million colonies, spread throughout the genome. In comparison to the CG-TTU colonies, the AT-TTU colonies were significantly more abundant and larger in size. Pure units and overlapping units of the pure units were readily detectable in the same colonies, signifying that the units are the sites of unequal crossover. Subsequently, we analyzed several of the AT-TTU colonies in several primates and mouse. We discovered dynamic sharedness of several of the colonies across the primate species, which mainly reached maximum complexity and size in human. In conclusion, we report massive crossover and recombination hotspots of the finest molecular resolution and evolutionary relevance in human. In respect of crossover and recombination, the human genome is far more dynamic than previously imagined.\u003c/p\u003e","manuscriptTitle":"Crossover and recombination hotspots massively spread across human genome","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-01-22 06:02:03","doi":"10.21203/rs.3.rs-3859914/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"740dde2c-d957-48ed-8a8e-cbbb432eabea","owner":[],"postedDate":"January 22nd, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":28263614,"name":"Biological sciences/Evolution"},{"id":28263615,"name":"Biological sciences/Genetics"}],"tags":[],"updatedAt":"2024-03-05T08:31:32+00:00","versionOfRecord":[],"versionCreatedAt":"2024-01-22 06:02:03","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-3859914","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-3859914","identity":"rs-3859914","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}