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Pangenome-resolved polymorphic transposable elements reveal human regulatory evolution in action

Jiang, J.; Zhuo, X.; Li, R.; Dong, Z.; Zhang, W.; Li, D.; Macias-Velasco, J.; Human Pangenome Reference Consortium, ; Wang, T.

2026-09-30 genetics
10.64898/2026.09.24.754167 bioRxiv
Show abstract

Transposable elements are a major source of gene-regulatory functions. Yet this contribution is understood largely from ancient insertions already fixed in the genome: the successes, seen long after the fact. The polymorphic phase before fixation or loss remains poorly resolved because such alleles could be scored only as present or absent. We resolved segregating transposable-element alleles as sequences, epigenetic states, and transcript components using 231 haplotype-resolved human pangenomes with matched long-read multi-omics. Their origins extend beyond recent transposition; their regulatory consequences depend on methylation and transcript context and are often missed by gene-level analyses; they provide mechanisms at trait-associated loci, while selection favors element presence and absence alike. Regulatory innovation before fixation is therefore not one-way accumulation, but a mixture of gain, remodeling, and loss.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.