Nanos downregulates maternal mRNAs in germline during Drosophila early embryogenesis

Nanos downregulates maternal mRNAs in germline during Drosophila early embryogenesis | bioRxiv /* */ /* */ <!-- <!-- /*! * yepnope1.5.4 * (c) WTFPL, GPLv2 */ (function(a,b,c){function d(a){return"[object Function]"==o.call(a)}function e(a){return"string"==typeof a}function f(){}function g(a){return!a||"loaded"==a||"complete"==a||"uninitialized"==a}function h(){var a=p.shift();q=1,a?a.t?m(function(){("c"==a.t?B.injectCss:B.injectJs)(a.s,0,a.a,a.x,a.e,1)},0):(a(),h()):q=0}function i(a,c,d,e,f,i,j){function k(b){if(!o&&g(l.readyState)&&(u.r=o=1,!q&&h(),l.onload=l.onreadystatechange=null,b)){"img"!=a&&m(function(){t.removeChild(l)},50);for(var d in y[c])y[c].hasOwnProperty(d)&&y[c][d].onload()}}var j=j||B.errorTimeout,l=b.createElement(a),o=0,r=0,u={t:d,s:c,e:f,a:i,x:j};1===y[c]&&(r=1,y[c]=[]),"object"==a?l.data=c:(l.src=c,l.type=a),l.width=l.height="0",l.onerror=l.onload=l.onreadystatechange=function(){k.call(this,r)},p.splice(e,0,u),"img"!=a&&(r||2===y[c]?(t.insertBefore(l,s?null:n),m(k,j)):y[c].push(l))}function j(a,b,c,d,f){return q=0,b=b||"j",e(a)?i("c"==b?v:u,a,b,this.i++,c,d,f):(p.splice(this.i++,0,a),1==p.length&&h()),this}function k(){var a=B;return a.loader={load:j,i:0},a}var l=b.documentElement,m=a.setTimeout,n=b.getElementsByTagName("script")[0],o={}.toString,p=[],q=0,r="MozAppearance"in l.style,s=r&&!!b.createRange().compareNode,t=s?l:n.parentNode,l=a.opera&&"[object Opera]"==o.call(a.opera),l=!!b.attachEvent&&!l,u=r?"object":l?"script":"img",v=l?"script":u,w=Array.isArray||function(a){return"[object Array]"==o.call(a)},x=[],y={},z={timeout:function(a,b){return b.length&&(a.timeout=b[0]),a}},A,B;B=function(a){function b(a){var a=a.split("!"),b=x.length,c=a.pop(),d=a.length,c={url:c,origUrl:c,prefixes:a},e,f,g;for(f=0;f<d;f++)g=a[f].split("="),(e=z[g.shift()])&&(c=e(c,g));for(f=0;f<b;f++)c=x[f](c);return c}function g(a,e,f,g,h){var i=b(a),j=i.autoCallback;i.url.split(".").pop().split("?").shift(),i.bypass||(e&&(e=d(e)?e:e[a]||e[g]||e[a.split("/").pop().split("?")[0]]),i.instead?i.instead(a,e,f,g,h):(y[i.url]?i.noexec=!0:y[i.url]=1,f.load(i.url,i.forceCSS||!i.forceJS&&"css"==i.url.split(".").pop().split("?").shift()?"c":c,i.noexec,i.attrs,i.timeout),(d(e)||d(j))&&f.load(function(){k(),e&&e(i.origUrl,h,g),j&&j(i.origUrl,h,g),y[i.url]=2})))}function h(a,b){function c(a,c){if(a){if(e(a))c||(j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}),g(a,j,b,0,h);else if(Object(a)===a)for(n in m=function(){var b=0,c;for(c in a)a.hasOwnProperty(c)&&b++;return b}(),a)a.hasOwnProperty(n)&&(!c&&!--m&&(d(j)?j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}:j[n]=function(a){return function(){var b=[].slice.call(arguments);a&&a.apply(this,b),l()}}(k[n])),g(a[n],j,b,n,h))}else!c&&l()}var h=!!a.test,i=a.load||a.both,j=a.callback||f,k=j,l=a.complete||f,m,n;c(h?a.yep:a.nope,!!i),i&&c(i)}var i,j,l=this.yepnope.loader;if(e(a))g(a,0,l,0);else if(w(a))for(i=0;i (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0];var j=d.createElement(s);var dl=l!='dataLayer'?'&l='+l:'';j.src='//www.googletagmanager.com/gtm.js?id='+i+dl;j.type='text/javascript';j.async=true;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-M677548'); Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search New Results Nanos downregulates maternal mRNAs in germline during Drosophila early embryogenesis View ORCID Profile Yasuhiro Kozono , Makoto Hayashi , View ORCID Profile Miho Asaoka , View ORCID Profile Satoru Kobayashi doi: https://doi.org/10.1101/2025.08.18.670776 Yasuhiro Kozono 1 Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba , Tsukuba, Ibaraki, 305-8577, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Yasuhiro Kozono Makoto Hayashi 2 Institute for Aquaculture Biotechnology (IAB), Tokyo University of Marine Science and Technology , 4-5-7, Konan, Minato-ku, Tokyo, 108-8477, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site Miho Asaoka 3 Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba, Ibaraki, 305-8577, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Miho Asaoka For correspondence: skob{at}tara.tsukuba.ac.jp masaoka{at}tara.tsukuba.ac.jp Satoru Kobayashi 1 Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba , Tsukuba, Ibaraki, 305-8577, Japan 3 Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba, Ibaraki, 305-8577, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Satoru Kobayashi For correspondence: skob{at}tara.tsukuba.ac.jp masaoka{at}tara.tsukuba.ac.jp Abstract Full Text Info/History Metrics Supplementary material Preview PDF SUMMARY Background Many maternal mRNAs in Drosophila primordial germ cells (PGCs) are degraded in concert with the synthesis of new transcripts from the zygotic genome during gastrulation and germ band elongation. However, few studies have focused on maternal mRNA destabilization in PGCs at the blastoderm stage that is prior to zygotic genome activation (ZGA). Thus, the stability of maternal mRNAs at this stage and regulation of their degradation remain poorly understood. To address this gap, we examined the role of Nanos, an RNA-binding protein known to promote mRNA degradation, in blastoderm-stage PGCs. Results By combining flow cytometry and RNA-seq analysis of PGCs, we identified the transcripts of 898 genes that were increased in nanos − PGCs. Among them, maternal mRNAs encoded by 298 genes were downregulated by Nanos in PGCs. Conclusions Our results show that Nanos downregulates maternal mRNA expression in PGCs before ZGA. As Nanos in C. elegans PGCs has also been reported to promote maternal-to-zygotic transition (MZT) via maternal mRNA downregulation during a transcriptionally silent state, our findings highlight the importance of investigating the function of Nanos for understanding the MZT in PGCs across various animal species. 1 INTRODUCTION During the maternal-to-zygotic transition (MZT), maternal mRNAs are degraded in concert with the synthesis of new transcripts from the zygotic genome. Several studies have shown that delays in their degradation impedes proper embryonic development 1 , 2 , indicating that maternal mRNA decay must be tightly regulated. In many animals, primordial germ cells (PGCs) are specified by inheriting factors localized in a specialized ooplasm, or germ plasm, which are required for their development. In Drosophila , PGCs are formed by incorporating the germ plasm, which harbors maternal mRNAs, and resides at the posterior pole of the blastoderm [1.5–3 h after egg laying (AEL)]. Massive maternal mRNA degradation and zygotic genome activation (ZGA) in PGCs during gastrulation and germ band elongation (3–5 h AEL) were first observed through transcriptomic and genetic analyses 1 , 3 , 4 . However, as few studies have focused on mRNA destabilization in blastoderm stage PGCs, maternal mRNA regulation in germline before ZGA remains poorly understood. Nanos is an evolutionarily conserved RNA-binding protein that promotes degradation and/or translational repression of mRNAs 5 – 7 . In Drosophila , Nanos forms a complex with the RNA-binding protein Pumilio (Pum), and binds to the Nanos–Pum motif, defined as WWWUGUA (W = A/U) 8 . During embryogenesis, Nanos is produced at the posterior pole immediately after egg deposition, transiently distributed in abdominal region at cleavage stage, and restricted to PGCs at blastoderm stage 9 . Nanos represses translation of hunchback ( hb ) mRNA in somatic regions, and of Cyclin B ( CycB ) and importin α2 ( impα2 ) mRNAs in blastoderm-stage PGCs 10 – 14 . The repression of CycB and impα2 are necessary for PGC development 10 , 12 , 15 , 16 . In addition, Nanos would broadly regulate maternal mRNAs. RNA-seq was performed on embryos harboring a fusion protein of Nanos and the nonsense-mediated decay (NMD) factor Upf1 17 . Given that tethering Upf1 to mRNAs induces their degradation. Using this system, they identified approximately 2,600 maternal mRNAs that were downregulated by Upf1-Nanos (Upf1-Nanos targets) 17 , indicating that these mRNAs are deposited maternally and potentially regulated by Nanos. Here, to identify maternal mRNAs that are actually downregulated by Nanos in PGCs, we purified PGCs from normal and nanos loss-of-function ( nanos - ) embryos at 2–3 h AEL, when the massive degradation of maternal mRNAs is not thought to have occurred, and performed RNA-seq analysis of these PGCs. 2 RESULTS AND DISCUSSION 2.1 Maternal mRNAs encoded by 298 genes were downregulated by Nanos in PGCs We performed RNA-seq analysis of PGCs from normal and nanos − embryos ( Figure 1A ). nanos mRNA was significantly reduced in nanos − PGCs compared to that in normal PGCs, demonstrating the reliability of our RNA-seq data. The mRNAs encoded by 898 genes were significantly increased in nanos − PGCs (Table S1). These mRNAs are thus downregulated in a Nanos-dependent manner. Among them, we found that maternal mRNAs encoded by 298 genes (Group I) were in the list of Upf1-Nanos targets (Table S2), while those encoded by 600 genes (Group II) were not. Download figure Open in new tab Figure 1. Transcriptome and RT-qPCR analyses for nanos- PGCs. (A) Volcano plot for normal vs nanos- PGCs. The thresholds for statistical significance were defined as FDR < 0.05 and log2FC ≥ 1 or ≤ −1. Magenta dots indicate the significantly increased mRNAs in nanos- PGC, and cyan dots indicate significantly decreased mRNAs. CycB mRNA was significantly increased in nanos -PGCs, while impα2 mRNA was not. (B) Log2 fold changes (log2FC) in nanos- /normal of CycB mRNA are presented. Significance was calculated by paired t -test. *P < 0.05. 2.2 The role of “Group I” mRNAs on PGC development To gain insights into Nanos function, we performed Gene Ontology (GO) analysis for “Group I” mRNAs (Table S3). Maternal mRNAs were enriched in terms related to the regulation of “GTPase activity”, suggesting that Nanos might play a role in controlling signal transduction. This GO category included somatic genes such as RhoGAP15B and Asap , which are involved in imaginal disc-derived leg morphogenesis and eye morphogenesis, respectively 18 , 19 . These results suggest that Nanos play a role in downregulation of somatic maternal mRNAs. A previous study has shown that nanos - PGCs can differentiate into somatic cells 20 ; this may be accounted for Nanos-mediated down regulation of somatic maternal mRNAs. 2.3 The enrichment of Nanos-Pum motif in both “Group I and II” mRNAs To know whether the “Group I” mRNAs are enriched for the binding motif of Nanos-Pum, we focused on Nanos-Pum motif, defined as WWWUGUA (W = A/U). This is motivated by several previous observations: (1) Nanos binds to the Nanos-Pum motif cooperatively with Pum 8 , based on SEQRS ( in vitro selection, high-throughput sequencing of RNA, and sequence specificity landscapes) analyses findings; (2) partial deletion of the Nanos-Pum motif (AUUGUA) from hb 3′-UTR abolishes Nanos-dependent mRNA degradation 6 , and (3) Upf1-Nanos targets are enriched for this motif 17 . We first identified Nanos-downregulated mRNA isoforms in PGCs because several mRNA isoforms are transcribed from a single gene. When we reanalyzed our data, 491 mRNA isoforms were found to be significantly upregulated in nanos − PGCs (Table S4). We next analyzed the proportion of mRNA isoforms that contain at least one Nanos-Pum motif and its density (the number of motifs per kilobase of 3′ UTR) 17 . As expected, we found that the “Group I” mRNAs showed significantly higher motif rates and densities compared to mRNAs that were not significantly altered in the presence and absence of Nanos ( Figure 2 ). Unexpectedly, this enrichment was also observed in “Group II” ( Figure 2 ), suggesting that these mRNAs may contain maternal transcripts regulated by Nanos in PGCs. This notion is supported by the fact that “Group II” contains CycB mRNA targeted by Nanos. CycB mRNA is known to be bound and translationally repressed by Nanos 8 , 10 , 11 . Furthermore, CycB mRNA is downregulated by Nanos in PGCs in our RNA-seq and RT-qPCR analyses ( Figure 1 ). Download figure Open in new tab Figure 2. The analyses Nanos-Pum motif. (A) the proportion of mRNAs that contain at least one Nanos-Pum motif was shown. NS: mRNAs with no significant change; I: “Group I” mRNAs; II: “Group II” mRNAs; III: mRNAs decreased in nanos − PGCs. Significance was calculated using Fisher’s exact test with Bonferroni correction. *P < 0.05. (B) The density of this motif (number per kilobase of 3′ UTR of this motif) was shown. Labels of each group were the same as in (A). Significance was assessed using the Steel–Dwass test. *P < 0.05. 2.4 Germline-specific function of Nanos in maternal mRNA destabilization The hb mRNA was included in “Group I” mRNAs (Table S2). Given that hb mRNA is also downregulated by Nanos in the somatic region 17 , it is likely that hb mRNA is regulated through a common mechanism in both soma and PGCs. In contrast, stability of CycB mRNA may be regulated through distinct mechanisms in soma and PGCs. Our results indicate that Nanos downregulates CycB mRNA in PGCs. However, previous RNA-seq analyses comparing normal and nanos − embryos did not detect significant differences in CycB mRNA levels 17 . Furthermore, it is suggested that CycB mRNA in somatic region is downregulated in a Smaug-dependent manner 21 . Smaug is a major factor for the clearance of maternal mRNAs in the soma 1 , 22 , and consistent with this, smaug mutants block the downregulation of CycB mRNA level 21 . This is the first study to report that Nanos downregulates a wide range of maternal mRNAs during early germline development. Immediately following the analyzed stage, massive maternal mRNA degradation and ZGA occur, suggesting that Nanos-mediated downregulation of maternal mRNAs is likely a part of the mechanism promoting MZT. In C. elegans PGCs, Nanos has been reported to facilitate MZT by downregulating maternal mRNAs during a transcriptionally repressed state 2 . Thus, investigating the function of Nanos will provide important perspectives for understanding the MZT in PGCs across various animals. Nanos-mediated mRNA downregulation under transcriptional repression occurs even in animals in which MZT does not occur in PGCs. In small micromeres of sea urchins (germline progenitors of Strongylocentrotus purpuratus ), MZT does not occur; however, these cells maintain transcriptional repression during the blastula stage, and Nanos depletes certain mRNAs 23 – 25 . These findings suggest that, in animals such as Drosophila, C. elegans , and sea urchins, where the germline undergoes early development with transcriptional repression, Nanos-mediated downregulation of mRNAs is a common feature. Therefore, this process is likely to play an important role during the early stages of development. 3 EXPERIMENTAL PROCEDURES 3.1 Fly strains Flies were maintained on standard Drosophila medium at 25°C. The following fly stocks were used: y w, nanos BN 9 , EGFP-vasa 26 . In the RNA-seq analysis, embryos produced from nanos BN EGFP-vasa / + and nanos BN EGFP-vasa / nanos BN females mated with y w were referred to as normal and nanos − , respectively. In the RT-qPCR analysis, embryos produced from EGFP-vasa /+ ; nanos BN / TM3 and EGFP-vasa /+ ; nanos BN / nanos BN females mated with y w were referred to as normal and nanos − , respectively. 3.2 RNA-seq analysis One hundred PGCs were isolated from 2 to 3 h AEL embryos using flow cytometry as described in a previous study 27 . cDNA was synthesized using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech, 634890) as described previously 15 , 28 . Nextera XT library creation and RNA-seq were performed at the University of Minnesota Genomics Center using a HiSeq 2500 platform (Illumina), and approximately 20 million reads per sample (50-bp paired-end reads) were obtained. Three biological replicates were used for each genotype. The corresponding raw read count data were deposited in the DNA Data Bank of Japan (DDBJ) under accession number DRR720111–DRR720116. Raw reads were processed using the Trimmomatic software (ver. 0.36) 29 and then aligned with HISAT2 (ver. 2.2.1) 30 to the BDGP D. melanogaster genome (dm6). The SAMtools software (ver. 1.9) 31 and StringTie (ver. 2.1.7) 32 were used to sort, merge, and count the reads. Count reads were processed using prepDE.py3 ( https://ccb.jhu.edu/software/stringtie/dl/prepDE.py3 ) and differential expression analysis was performed using the edgeR package (ver. 4.0.16) 33 , 34 of R (ver. 4.3.3). For quality control of our dataset, the transcripts showing count-per-million > 0.5 in at least three samples were filtered and then normalized by the trimmed-mean method before differential expression analysis. Differentially expressed transcripts were identified by comparing the normal and nanos − dataset using likelihood ratio test. GO functional enrichment analysis was performed using Metascape (ver. 3.5) 35 . The detected transcripts were used as the background, and the significantly increased and decreased transcripts in nanos − were analyzed separately. To identify differentially expressed transcripts, the thresholds for statistical significance between normal and nanos − PGCs were defined as FDR < 0.05 and log2FC ≥ 1 or ≤ −1. Subsequently, a list of all 3′-UTR sequences (FlyBase; dmel-all-three_prime_UTR-r6.61.fasta) was obtained. The 3′-UTR list was merged with the dataset of differentially expressed transcripts, and then the proportion and density of Nanos-Pum motif were calculated. 3.3 RT-qPCR analysis One hundred PGCs were isolated from 2 to 3 h AEL embryos using flow cytometry as described in a previous study 27 . The isolated PGCs were sorted into PCR tubes preloaded with 4 μL of a lysis solution comprising RNase-free water (Takara Bio), 0.3% NP-40 (Thermo Fisher Scientific), and RNasin Plus at 1 U/μL (Promega). The tubes were mixed using MixMate (Eppendorf) at 2000 rpm for 30 s, followed by brief centrifugation at 4°C. cDNA was synthesized from the lysate using the Superscript VILO Master Mix (Thermo Fisher Scientific). Quantification was performed on a Light Cycler 480 system (Roche) using a QuantiTect SYBR Green RT-PCR Kit (QIAGEN). The primer sets used for qPCR are listed in Table S5. Thermal cycling conditions were as follows: one cycle of 95°C for 15 m, then 45 cycles of 95°C for 15 s and 60°C for 1 m. Fluorescence in each well was monitored throughout the cycling period. Melting curve analysis was performed to evaluate off-target amplification. Data were analyzed using the Light Cycler software (Roche) and Microsoft Excel (Microsoft). Using the ΔΔC T method 36 , values were normalized against those of Actin 5C ( Act5C ), and log2 expression ratios were calculated. Statistical significance was calculated by paired t -test. CONFLICT OF INTEREST STATEMENT The authors declare no conflicts of interest. ACKNOWLEDGEMENT This work was supported in part by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science, Japan (JSPS) [KAKENHI Grant Numbers: 24H02030 (SK) and 23K05778 (MA)] and Japan Science and Technology Agency, Japan (JST) [Support for Pioneering Research Initiated by the Next Generation (SPRING) Grant Numbers: JPMJSP2124 (YK)]. We thank Dr. Shunta Yorimoto for technical advice of RNA-seq analysis. Funder Information Declared Japan Society for the Promotion of Science, https://ror.org/00hhkn466 , 24H02030 , 23K05778 Japan Science and Technology Agency, https://ror.org/00097mb19 , JPMJSP2124 Footnotes Grant support information: Scientific Research from the Japan Society for the Promotion of Science, Japan (JSPS) [KAKENHI Grant Numbers: 24H02030 (SK) and 23K05778 (MA)] and Japan Science and Technology Agency, Japan (JST) [Support for Pioneering Research Initiated by the Next Generation (SPRING) Grant Numbers: JPMJSP2124 (YK)] REFERENCES 1. ↵ Laver JD , Marsolais AJ , Smibert CA , Lipshitz HD . Regulation and function of maternal gene products during the maternal-to-zygotic transition in Drosophila. Lipshitz HD , ed. Curr Top Dev Biol . 2015 ; 113 : 43 – 84 . OpenUrl CrossRef PubMed 2. ↵ Lee CYS , Lu T , Seydoux G. Nanos promotes epigenetic reprograming of the germline by down-regulation of the THAP transcription factor LIN-15B . Elife . 2017 ; 6 : e30201 . OpenUrl CrossRef PubMed 3. ↵ Siddiqui NU , Li X , Luo H , et al. Genome-wide analysis of the maternal-to-zygotic transition in Drosophila primordial germ cells . Genome Biol . 2012 ; 13 ( 2 ): R11 . OpenUrl CrossRef PubMed 4. ↵ Van Doren M , Williamson AL , Lehmann R. Regulation of zygotic gene expression in Drosophila primordial germ cells . Curr Biol . 1998 ; 8 ( 4 ): 243 – 246 . OpenUrl CrossRef PubMed Web of Science 5. ↵ Oulhen N , Wessel GM . Every which way--nanos gene regulation in echinoderms: Nanos Gene Regulation in Echinoderms . Genesis . 2014 ; 52 ( 3 ): 279 – 286 . OpenUrl PubMed 6. ↵ Raisch T , Bhandari D , Sabath K , et al. Distinct modes of recruitment of the CCR4-NOT complex by Drosophila and vertebrate Nanos . EMBO J . 2016 ; 35 ( 9 ): 974 – 990 . OpenUrl Abstract / FREE Full Text 7. ↵ Bhandari D , Raisch T , Weichenrieder O , Jonas S , Izaurralde E. Structural basis for the Nanos-mediated recruitment of the CCR4-NOT complex and translational repression . Genes Dev . 2014 ; 28 ( 8 ): 888 – 901 . OpenUrl Abstract / FREE Full Text 8. ↵ Weidmann CA , Qiu C , Arvola RM , et al. Drosophila Nanos acts as a molecular clamp that modulates the RNA-binding and repression activities of Pumilio . Elife . 2016 ; 5 : e17096 . OpenUrl CrossRef PubMed 9. ↵ Wang C , Dickinson LK , Lehmann R. Genetics of nanos localization in Drosophila . Dev Dyn . 1994 ; 199 ( 2 ): 103 – 115 . OpenUrl CrossRef PubMed Web of Science 10. ↵ Asaoka-Taguchi M , Yamada M , Nakamura A , Hanyu K , Kobayashi S. Maternal Pumilio acts together with Nanos in germline development in Drosophila embryos . Nat Cell Biol . 1999 ; 1 ( 7 ): 431 – 437 . OpenUrl CrossRef PubMed Web of Science 11. ↵ Kadyrova LY , Habara Y , Lee TH , Wharton RP . Translational control of maternal Cyclin B mRNA by Nanos in the Drosophila germline . Development . 2007 ; 134 ( 8 ): 1519 – 1527 . OpenUrl Abstract / FREE Full Text 12. ↵ Asaoka M , Hanyu-Nakamura K , Nakamura A , Kobayashi S. Maternal Nanos inhibits Importin-α2/Pendulin-dependent nuclear import to prevent somatic gene expression in the Drosophila germline . PLoS Genet . 2019 ; 15 ( 5 ): e1008090 . OpenUrl CrossRef PubMed 13. Wharton RP , Struhl G. RNA regulatory elements mediate control of Drosophila body pattern by the posterior morphogen nanos . Cell . 1991 ; 67 ( 5 ): 955 – 967 . OpenUrl CrossRef PubMed Web of Science 14. ↵ Murata Y , Wharton RP . Binding of pumilio to maternal hunchback mRNA is required for posterior patterning in Drosophila embryos . Cell . 1995 ; 80 ( 5 ): 747 – 756 . OpenUrl CrossRef PubMed Web of Science 15. ↵ Morita S , Ota R , Hayashi M , Kobayashi S. Repression of G1/S transition by transient inhibition of miR-10404 expression in Drosophila primordial germ cells . iScience . 2020 ; 23 ( 3 ): 100950 . OpenUrl PubMed 16. ↵ Asaoka M , Kayama M , Kawagoe T , Hayashi M , Morita S , Kobayashi S. Somatic gene repression ensures physical segregation of germline and soma in Drosophila embryos . bioRxiv . Published online June 15, 2025:2025.06.13.659480. doi: 10.1101/2025.06.13.659480 OpenUrl Abstract / FREE Full Text 17. ↵ Marhabaie M , Wharton TH , Kim SY , Wharton RP . Widespread regulation of the maternal transcriptome by Nanos in Drosophila . PLoS Biol . 2024 ; 22 ( 10 ): e3002840 . OpenUrl CrossRef PubMed 18. ↵ Greenberg L , Hatini V. Systematic expression and loss-of-function analysis defines spatially restricted requirements for Drosophila RhoGEFs and RhoGAPs in leg morphogenesis . Mech Dev . 2011 ; 128 ( 1-2 ): 5 – 17 . OpenUrl CrossRef PubMed 19. ↵ Johnson RI , Sedgwick A , D’Souza-Schorey C , Cagan RL . Role for a Cindr-Arf6 axis in patterning emerging epithelia . Mol Biol Cell . 2011 ; 22 ( 23 ): 4513 – 4526 . OpenUrl Abstract / FREE Full Text 20. ↵ Hayashi Y , Hayashi M , Kobayashi S. Nanos suppresses somatic cell fate in Drosophila germ line . Proc Natl Acad Sci U S A . 2004 ; 101 ( 28 ): 10338 – 10342 . OpenUrl Abstract / FREE Full Text 21. ↵ Benoit B , He CH , Zhang F , et al. An essential role for the RNA-binding protein Smaug during the Drosophila maternal-to-zygotic transition . Development . 2009 ; 136 ( 6 ): 923 – 932 . OpenUrl Abstract / FREE Full Text 22. ↵ Tadros W , Goldman AL , Babak T , et al. SMAUG is a major regulator of maternal mRNA destabilization in Drosophila and its translation is activated by the PAN GU kinase . Dev Cell . 2007 ; 12 ( 1 ): 143 – 155 . OpenUrl CrossRef PubMed Web of Science 23. ↵ Swartz SZ , Reich AM , Oulhen N , et al. Deadenylase depletion protects inherited mRNAs in primordial germ cells . Development . 2014 ; 141 ( 16 ): 3134 – 3142 . OpenUrl Abstract / FREE Full Text 24. Swartz SZ , Wessel GM . Germ line versus Soma in the transition from egg to embryo. Lipshitz HD , ed. Curr Top Dev Biol . 2015 ; 113 : 149 – 190 . OpenUrl CrossRef PubMed 25. ↵ Oulhen N , Swartz SZ , Laird J , Mascaro A , Wessel GM . Transient translational quiescence in primordial germ cells . Development . 2017 ; 144 ( 7 ): 1201 – 1210 . OpenUrl Abstract / FREE Full Text 26. ↵ Sano H , Nakamura A , Kobayashi S. Identification of a transcriptional regulatory region for germline-specific expression of vasa gene in Drosophila melanogaster . Mech Dev . 2002 ; 112 ( 1-2 ): 129 – 139 . OpenUrl CrossRef PubMed Web of Science 27. ↵ Shigenobu S , Arita K , Kitadate Y , Noda C , Kobayashi S. Isolation of germline cells from Drosophila embryos by flow cytometry . Dev Growth Differ . 2006 ; 48 ( 1 ): 49 – 57 . OpenUrl CrossRef PubMed Web of Science 28. ↵ Shigenobu S , Kitadate Y , Noda C , Kobayashi S. Molecular characterization of embryonic gonads by gene expression profiling in Drosophila melanogaster . Proc Natl Acad Sci U S A . 2006 ; 103 ( 37 ): 13728 – 13733 . OpenUrl Abstract / FREE Full Text 29. ↵ Bolger AM , Lohse M , Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data . Bioinformatics . 2014 ; 30 ( 15 ): 2114 – 2120 . OpenUrl CrossRef PubMed Web of Science 30. ↵ Kim D , Paggi JM , Park C , Bennett C , Salzberg SL . Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype . Nat Biotechnol . 2019 ; 37 ( 8 ): 907 – 915 . OpenUrl CrossRef PubMed 31. ↵ Li H , Handsaker B , Wysoker A , et al. The Sequence Alignment/Map format and SAMtools . Bioinformatics . 2009 ; 25 ( 16 ): 2078 – 2079 . OpenUrl CrossRef PubMed Web of Science 32. ↵ Pertea M , Kim D , Pertea GM , Leek JT , Salzberg SL . Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown . Nat Protoc . 2016 ; 11 ( 9 ): 1650 – 1667 . OpenUrl CrossRef PubMed 33. ↵ Robinson MD , McCarthy DJ , Smyth GK . edgeR: a Bioconductor package for differential expression analysis of digital gene expression data . Bioinformatics . 2010 ; 26 ( 1 ): 139 – 140 . OpenUrl CrossRef PubMed Web of Science 34. ↵ McCarthy DJ , Chen Y , Smyth GK . Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation . Nucleic Acids Res . 2012 ; 40 ( 10 ): 4288 – 4297 . OpenUrl CrossRef PubMed Web of Science 35. ↵ Zhou Y , Zhou B , Pache L , et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets . Nat Commun . 2019 ; 10 ( 1 ): 1523 . OpenUrl CrossRef PubMed 36. ↵ Livak KJ , Schmittgen TD . Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT Method . Methods . 2001 ; 25 ( 4 ): 402 – 408 . OpenUrl CrossRef PubMed Web of Science View the discussion thread. Back to top Previous Next Posted August 22, 2025. Download PDF Supplementary Material Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. You are going to email the following Nanos downregulates maternal mRNAs in germline during Drosophila early embryogenesis Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website. Your Personal Message CAPTCHA This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. Share Nanos downregulates maternal mRNAs in germline during Drosophila early embryogenesis Yasuhiro Kozono , Makoto Hayashi , Miho Asaoka , Satoru Kobayashi bioRxiv 2025.08.18.670776; doi: https://doi.org/10.1101/2025.08.18.670776 Share This Article: Copy Citation Tools Nanos downregulates maternal mRNAs in germline during Drosophila early embryogenesis Yasuhiro Kozono , Makoto Hayashi , Miho Asaoka , Satoru Kobayashi bioRxiv 2025.08.18.670776; doi: https://doi.org/10.1101/2025.08.18.670776 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Area Developmental Biology Subject Areas All Articles Animal Behavior and Cognition (7629) Biochemistry (17660) Bioengineering (13881) Bioinformatics (41911) Biophysics (21436) Cancer Biology (18578) Cell Biology (25482) Clinical Trials (138) Developmental Biology (13371) Ecology (19887) Epidemiology (2067) Evolutionary Biology (24302) Genetics (15599) Genomics (22483) Immunology (17728) Microbiology (40364) Molecular Biology (17163) Neuroscience (88537) Paleontology (666) Pathology (2830) Pharmacology and Toxicology (4821) Physiology (7637) Plant Biology (15129) Scientific Communication and Education (2045) Synthetic Biology (4290) Systems Biology (9817) Zoology (2269)