Pangenome-resolved polymorphic transposable elements reveal human regulatory evolution in action
- 1Washington University in St Louis
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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BibTeX
@misc{jiang2026pangenomeresolved,
title = {{Pangenome-resolved polymorphic transposable elements reveal human regulatory evolution in action}},
author = {J. Jiang and X. Zhuo and R. Li and Z. Dong and W. Zhang and D. Li and J. Macias-Velasco and Human Pangenome Reference Consortium and T. Wang},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.24.754167},
url = {https://www.biorxiv.org/content/10.64898/2026.09.24.754167v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Pangenome-resolved polymorphic transposable elements reveal human regulatory evolution in action
AU - J. Jiang
AU - X. Zhuo
AU - R. Li
AU - Z. Dong
AU - W. Zhang
AU - D. Li
AU - J. Macias-Velasco
AU - Human Pangenome Reference Consortium
AU - T. Wang
PY - 2026
DA - 2026/09/24
PB - bioRxiv
DO - 10.64898/2026.09.24.754167
UR - https://www.biorxiv.org/content/10.64898/2026.09.24.754167v1
AB - 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.
ER -