Two-repeat units of CG-rich trinucleotides form long-sought hotspot loci shared across primates and mouse

Two-repeat units of CG-rich trinucleotides form long-sought hotspot loci shared across primates and mouse | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (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],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Two-repeat units of CG-rich trinucleotides form long-sought hotspot loci shared across primates and mouse Mina Ohadi, Nahid Tajeddin, Hadi Bayat, Masoud Arabfard, Ali M. A. Maddi, and 5 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3288256/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background CG-rich trinucleotide short tandem repeats link with human cognition and various neurodevelopmental, neurological, and movement disorders. However, the fundamental two-repeat units of these STRs are literally unexplored. Results On a genome-wide scale, here we mapped the two-repeat units of all combinations of trinucleotides in human, and found thousands of colonies (distance between each unit < 500 bp) of exceedingly significant occurrence based on Poisson distribution. Subsequently, we performed a comparative genomics study of several of the large and medium-size colonies in other primates and mouse. We discovered that some of those colonies were shared with extensive dynamicity, as phylogenetically distant as in mouse. We found evidence of emergence and propagation of several non-coding RNAs, such as PIWI-interacting RNAs (piRNAs) and uncharacterized RNAs in some colonies. Conclusion We report evidence of extensively dynamic trans-species crossing-over and conversion events in the two-repeat unit colonies of CG-rich trinucleotides, which among many evolutionary implications, may be a novel mechanism for the emergence and propagation of non-coding RNAs in some colonies. This is the first evidence of loci of massive genomic hotspot events, shared at least across primates and mouse. Biological sciences/Computational biology and bioinformatics Biological sciences/Evolution Biological sciences/Genetics Biological sciences/Molecular biology Human Primate Mouse CG-rich trinucleotide Hotspot Shared loci Evolution Full Text 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. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. 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-3288256","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":228407916,"identity":"a8c54938-dbf4-4022-af8d-ad9020058d1a","order_by":0,"name":"Mina Ohadi","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAxElEQVRIiWNgGAWjYDACZgji4UcWIU6LZAPRWmC6DA4Q6y7ddgbGxwU11jLGN9KfSVcw2MkzsPM+wKvF7DADs/GMY+k8ZjdyzCTPMCQbNjCzGxDSwibNw3YYpIXtZgMDcwIDMxt+h0G0/DvMYzwj/RlQSz2RWnjbDvMYSCSYAbUcJkYLY7Mxb186j8SZN+Y/GwyOG7YR1HL+8MHHPN+s7fnb0x8bNlRUy/PzH8OvhYGBsQGJAwwrAnaMglEwCkbBKCAGAADpGDRPieoiBAAAAABJRU5ErkJggg==","orcid":"","institution":"University of Social Welfare and Rehabilitation Sciences","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Mina","middleName":"","lastName":"Ohadi","suffix":""},{"id":228407918,"identity":"8f2f07d2-2594-47ea-a2f8-ffa80c5b8567","order_by":1,"name":"Nahid Tajeddin","email":"","orcid":"","institution":"University of Social Welfare and Rehabilitation Sciences","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Nahid","middleName":"","lastName":"Tajeddin","suffix":""},{"id":228407920,"identity":"435078ca-4686-4913-b728-6e7fc599a9fa","order_by":2,"name":"Hadi Bayat","email":"","orcid":"","institution":"University of Social Welfare and Rehabilitation Sciences","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Hadi","middleName":"","lastName":"Bayat","suffix":""},{"id":228407922,"identity":"76bacc7a-79e6-47ac-9210-4b99a2e8e4c0","order_by":3,"name":"Masoud Arabfard","email":"","orcid":"","institution":"Baqiyatallah University of Medical Sciences","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Masoud","middleName":"","lastName":"Arabfard","suffix":""},{"id":228407924,"identity":"36408d6c-e635-4647-983f-aaf9b9c5a8fd","order_by":4,"name":"Ali M. 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However, the fundamental two-repeat units of these STRs are literally unexplored.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e \u003cp\u003eOn a genome-wide scale, here we mapped the two-repeat units of all combinations of trinucleotides in human, and found thousands of colonies (distance between each unit\u0026thinsp;\u0026lt;\u0026thinsp;500 bp) of exceedingly significant occurrence based on Poisson distribution. Subsequently, we performed a comparative genomics study of several of the large and medium-size colonies in other primates and mouse. We discovered that some of those colonies were shared with extensive dynamicity, as phylogenetically distant as in mouse. We found evidence of emergence and propagation of several non-coding RNAs, such as PIWI-interacting RNAs (piRNAs) and uncharacterized RNAs in some colonies.\u003c/p\u003e\u003ch2\u003eConclusion\u003c/h2\u003e \u003cp\u003eWe report evidence of extensively dynamic trans-species crossing-over and conversion events in the two-repeat unit colonies of CG-rich trinucleotides, which among many evolutionary implications, may be a novel mechanism for the emergence and propagation of non-coding RNAs in some colonies. 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