Regulatory transposable elements in the encyclopedia of DNA elements.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
31 Aug 2024
31 Aug 2024
Historique:
received:
07
10
2023
accepted:
16
08
2024
medline:
1
9
2024
pubmed:
1
9
2024
entrez:
31
8
2024
Statut:
epublish
Résumé
Transposable elements (TEs) comprise ~50% of our genome, but knowledge of how TEs affect genome evolution remains incomplete. Leveraging ENCODE4 data, we provide the most comprehensive study to date of TE contributions to the regulatory genome. We find 236,181 (~25%) human candidate cis-regulatory elements (cCREs) are TE-derived, with over 90% lineage-specific since the human-mouse split, accounting for 8-36% of lineage-specific cCREs. Except for SINEs, cCRE-associated transcription factor (TF) motifs in TEs are derived from ancestral TE sequence more than expected by chance. We show that TEs may adopt similar regulatory activities of elements near their integration site. Since human-mouse divergence, TEs have contributed 3-56% of TF binding site turnover events across 30 examined TFs. Finally, TE-derived cCREs are similar to non-TE cCREs in terms of MPRA activity and GWAS variant enrichment. Overall, our results substantiate the notion that TEs have played an important role in shaping the human regulatory genome.
Identifiants
pubmed: 39217141
doi: 10.1038/s41467-024-51921-6
pii: 10.1038/s41467-024-51921-6
doi:
Substances chimiques
DNA Transposable Elements
0
Transcription Factors
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
7594Subventions
Organisme : U.S. Department of Health & Human Services | National Institutes of Health (NIH)
ID : R01HG007175
Organisme : U.S. Department of Health & Human Services | National Institutes of Health (NIH)
ID : U01HG009391
Organisme : U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)
ID : T32HG000045
Organisme : U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
ID : 2R35GM122550-06
Informations de copyright
© 2024. The Author(s).
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