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The complete telomere-to-telomere (T2T) assembly enables comprehensive investigation of TE contributions to gene regulation. Using a 10 kb window around transcription start sites, we mapped 3,709,429 human TEs to 28,738 genes against a 500-permutation background and assessed the enrichment and functional associations of 6 TE classes and 44 families. We identified a 220 kb interferon-alpha domain enriched with young L1 elements: 77 of its 175 TEs are evolutionary young L1 copies from 36 subfamilies, at mean divergence 135.7 against 188.2 genome-wide. This is consistent with recent L1 activity and could indicate a recent evolutionary arms-race affecting innate immune gene regulation. Distinct TE classes exhibited specific functional associations: SVA elements were enriched near genes involved in transcription termination; Alu elements were linked to RNA processing and splicing; MIR elements were associated with zinc homeostasis and voltage-gated potassium channel genes; LINE elements were enriched near genes related to lipid metabolism and olfactory perception; and LTR elements were associated with ion transport. This correlative map provides a positional baseline against which epigenomic and functional TE studies can be normalized, and a set of candidate loci for further investigation of evolutionary arms race.<\/jats:p>","DOI":"10.1093\/g3journal\/jkag250","type":"journal-article","created":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T18:24:05Z","timestamp":1790187845000},"source":"Crossref","is-referenced-by-count":0,"title":["Telomere-to-telomere co-mapping of transposable elements and human genes identifies a cluster of young L1 elements in the interferon-alpha domain with potential evolutionary arms-race"],"prefix":"10.1093","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1029-1174","authenticated-orcid":false,"given":"Daniil","family":"Nikitin","sequence":"first","affiliation":[{"name":"Institute of Molecular Biology, National Academy of Science of the Republic of Armenia , Yerevan 0014, Republic of 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