Attention note: Data reanalysis DNA Transposons Favor de novo Transcript Emergence Through Enrichment of Transcription Factor Binding Motifs

Attention note: Data reanalysis DNA Transposons Favor de novo Transcript Emergence Through Enrichment of Transcription Factor Binding Motifs | 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 Data Note Attention note: Data reanalysis DNA Transposons Favor de novo Transcript Emergence Through Enrichment of Transcription Factor Binding Motifs Marie Kristin Lebherz, Bertrand Fouks, Erich Bornberg-Bauer, Anna Grandchamp This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9616708/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 In a previous study, we investigated the contribution of transposable elements (TEs) to the emergence of de novo transcripts in seven inbred lines of Drosophila melanogaster. We showed that de novo transcripts overlap TEs more frequently than expected by chance and that their upstream regions are enriched in regulatory motifs, particularly when overlapping TEs. Based on the TE annotations available at the time, DNA transposons appeared to be the class most strongly associated with the emergence of de novo transcripts. Subsequent to publication, we were informed that the software used for TE annotation may misclassify certain TEs as DNA transposons. To assess this issue, we reannotated TEs in all seven lines using four alternative annotation tools and repeated all downstream analyses. While the association between de novo transcripts and TE insertions remains robust, the identity of the TE families involved varies substantially across annotation methods. In contrast to our original conclusions, three of the four alternative tools indicate a stronger enrichment of RNA transposons than DNA transposons at de novo transcript loci. These results highlight the sensitivity of TE-based inferences to annotation methodology and underscore the need for continued improvements in TE detection tools. Evolutionary Biology Bioinformatics Transposable elements de novo transcripts Drosophila melanogaster Full Text Additional Declarations The authors declare no competing interests. Supplementary Files Suppdata.pdf 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-9616708","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Data Note","associatedPublications":[],"authors":[{"id":634685635,"identity":"7b46d77a-d0d1-431d-a49a-33aad3944add","order_by":0,"name":"Marie Kristin Lebherz","email":"","orcid":"https://orcid.org/0009-0009-4592-3179","institution":"Institute for Evolution and Biodiversity, University of Münster, Münster, Germany","correspondingAuthor":false,"prefix":"","firstName":"Marie","middleName":"Kristin","lastName":"Lebherz","suffix":""},{"id":634687962,"identity":"7088137b-48a4-4b22-9810-fea2593e90fd","order_by":1,"name":"Bertrand 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We showed that de novo transcripts overlap TEs more frequently than expected by chance and that their upstream regions are enriched in regulatory motifs, particularly when overlapping TEs. Based on the TE annotations available at the time, DNA transposons appeared to be the class most strongly associated with the emergence of de novo transcripts.\u003c/p\u003e\n\u003cp\u003eSubsequent to publication, we were informed that the software used for TE annotation may misclassify certain TEs as DNA transposons. To assess this issue, we reannotated TEs in all seven lines using four alternative annotation tools and repeated all downstream analyses.\u003c/p\u003e\n\u003cp\u003eWhile the association between de novo transcripts and TE insertions remains robust, the identity of the TE families involved varies substantially across annotation methods. In contrast to our original conclusions, three of the four alternative tools indicate a stronger enrichment of RNA transposons than DNA transposons at de novo transcript loci. 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