Supplementary Material for Nikitin, 2026

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 six 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.