Datasets and Scripts associated with "Cryptic endogenous retrovirus subfamilies in the primate lineage"

Scripts and datasets included here were used for the main analyses in the study of "Cryptic endogenous retrovirus subfamilies in the primate lineage".

Study 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 evolutionarily young LTR subfamilies known as MER11A/B/C, we revealed the presence of four ‘new subfamilies’, that better explain 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 ape-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.