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bioRxiv · 10.1101/2023.12.07.570592

Cryptic endogenous retrovirus subfamilies in the primate lineage

Chen, X.·Zhang, Z.·Yan, Y.·Goubert, C.·Bourque, G.·Inoue, F.
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Abstract

Many endogenous retroviruses (ERVs) in the human genome are primate-specific and have contributed novel cis-regulatory elements and transcripts. However, current approaches for classifying and annotating ERVs and their long terminal repeats (LTRs) have limited resolution and are inaccurate. Here, we developed a new annotation based on phylogenetic analysis and cross-species conservation. Focusing on the evolutionary young MER11A/B/C subfamilies, we revealed the presence of 4 new subfamilies, that better explained the epigenetic heterogeneity observed within the MER11 instances, suggesting a new annotation for 412 (19.8%) of these repeat elements. Furthermore, we functionally validated the regulatory potential of these four new subfamilies using a massively parallel reporter assay (MPRA), which also identified motifs associated with their differential activities. Combining MPRA with new annotations across primates revealed an apes-specific gain of SOX related motifs through a single-nucleotide deletion. Lastly, by applying our approach across 53 simian-enriched LTR subfamilies, we defined a total of 75 new subfamilies and found that 3,807 (30.0%) instances from 26 LTR subfamilies could be categorized into a novel annotation, many of which with a distinct epigenetic profile. Thus, with our refined annotation of simian-enriched LTRs, it will be possible to better understand the evolution in primate genomes and potentially identify new roles for ERVs and their LTRs in the hosts.

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Chen, X., Zhang, Z., Yan, Y., Goubert, C., Bourque, G., Inoue, F.. 2023-12-08. Cryptic endogenous retrovirus subfamilies in the primate lineage. https://doi.org/10.1101/2023.12.07.570592

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