IAP retrotransposons contribute to the transcriptional diversity of the murine placenta

IAP retrotransposons contribute to the transcriptional diversity of the murine placenta | bioRxiv Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search New Results IAP retrotransposons contribute to the transcriptional diversity of the murine placenta View ORCID Profile Samuele M. Amante , View ORCID Profile Maria L. Vignola , View ORCID Profile Cyril Pulver , View ORCID Profile Tessa M. Bertozzi , Anne C. Ferguson-Smith , View ORCID Profile Marika Charalambous , View ORCID Profile Miguel R. Branco doi: https://doi.org/10.64898/2026.01.27.702056 Samuele M. Amante 1 Blizard Institute, Faculty of Medicine and Dentistry , QMUL, London, UK 2 Centre for Epigenetics , QMUL, London, UK Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Samuele M. Amante For correspondence: s.amante{at}qmul.ac.uk m.branco{at}qmul.ac.uk Maria L. Vignola 3 Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London , London, United Kingdom Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Maria L. Vignola Cyril Pulver 4 School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL) , CH-1015, Lausanne, Switzerland Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Cyril Pulver Tessa M. Bertozzi 5 Department of Genetics, University of Cambridge , Cambridge, UK 6 Whitehead Institute for Biomedical Research , Cambridge, MA, USA Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Tessa M. Bertozzi Anne C. Ferguson-Smith 5 Department of Genetics, University of Cambridge , Cambridge, UK Find this author on Google Scholar Find this author on PubMed Search for this author on this site Marika Charalambous 3 Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London , London, United Kingdom Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Marika Charalambous Miguel R. Branco 1 Blizard Institute, Faculty of Medicine and Dentistry , QMUL, London, UK 2 Centre for Epigenetics , QMUL, London, UK Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Miguel R. Branco For correspondence: s.amante{at}qmul.ac.uk m.branco{at}qmul.ac.uk Abstract Full Text Info/History Metrics Supplementary material Data/Code Preview PDF Abstract Transposable elements (TEs) have made important contributions to the evolution of the placenta, and are argued to have played a role in the wide inter-species diversification of this critical developmental organ. Co-option of TEs by host genomes has led to the genesis of important placental genes, as well as trophoblast-specific gene regulatory elements. But whilst multiple TE subfamilies have been shown to act as transcriptional enhancers in early mouse trophoblast development, it remains unclear to what extent TEs regulate placental gene expression after the establishment of a functional fetal-maternal interface. Here, we characterised the TE regulatory and transcriptional landscape in mouse placenta and gauged their evolutionary dynamics through a comparative approach. We found that overall, the gene regulatory potential of TEs is greatly diminished in differentiated mouse trophoblast when compared to their stem cell counterpart. However, evolutionarily young intracisternal A particle (IAP) elements are highly expressed in the placenta and create several alternative, placenta-specific transcriptional start sites for protein-coding genes. IAP elements that are active in the placenta drive species-specific expression of associated genes and display wide genetic diversity between mouse strains. These putative co-option events are therefore evolutionarily recent and may represent a prime example of how TE activity can drive fast placental evolution. Competing Interest Statement The authors have declared no competing interest. Footnotes In response to the reviewers' comments, we have made the following revisions to the manuscript: -Added new CUT&Tag data from in vitro differentiated trophoblast stem cells (TSCs) for a more direct comparison with data from undifferentiated cells (Figures 1B, 1C, S1C). - Clarified the conditions for TSC culture and differentiation (Methods section) and added RT-qPCR data to characterise our in-house derived TSC line (Figure S1A). - Added a better explanation of the rationale and method used to analyse CUT&Tag data. - Added new western blot data for SUV39H2 (Figure S5) to query the possibility of a longer protein isoform being produced in the placenta. - Performed transcription factor binding motif analysis on IAP elements to identify a putative transcription factor involved in driving cell type-specific IAP expression (Figure S3C). - Made multiple changes to the text to improve readability and correct typos. - Corrected missing information in the list of references. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE316744 https://github.com/MBrancoLab/Amante_2026_mPlacenta Funder Information Declared Biotechnology and Biological Sciences Research Council , BB/T000031/1 , BB/X007758/1 Medical Research Council , MR/X008487/1 Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license . Back to top Previous Next Posted September 15, 2026. Download PDF Supplementary Material Data/Code 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 IAP retrotransposons contribute to the transcriptional diversity of the murine placenta 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 IAP retrotransposons contribute to the transcriptional diversity of the murine placenta Samuele M. Amante , Maria L. Vignola , Cyril Pulver , Tessa M. Bertozzi , Anne C. Ferguson-Smith , Marika Charalambous , Miguel R. Branco bioRxiv 2026.01.27.702056; doi: https://doi.org/10.64898/2026.01.27.702056 Share This Article: Copy Citation Tools IAP retrotransposons contribute to the transcriptional diversity of the murine placenta Samuele M. Amante , Maria L. Vignola , Cyril Pulver , Tessa M. Bertozzi , Anne C. Ferguson-Smith , Marika Charalambous , Miguel R. Branco bioRxiv 2026.01.27.702056; doi: https://doi.org/10.64898/2026.01.27.702056 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 Genetics Subject Areas All Articles Animal Behavior and Cognition (8164) Biochemistry (19027) Bioengineering (15171) Bioinformatics (45808) Biophysics (22958) Cancer Biology (20248) Cell Biology (27495) Clinical Trials (138) Developmental Biology (14233) Ecology (21529) Epidemiology (2067) Evolutionary Biology (25940) Genetics (16436) Genomics (23979) Immunology (19176) Microbiology (43488) Molecular Biology (18483) Neuroscience (95839) Paleontology (717) Pathology (3064) Pharmacology and Toxicology (5253) Physiology (8339) Plant Biology (16378) Scientific Communication and Education (2123) Synthetic Biology (4675) Systems Biology (10451) Zoology (2436)

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