
==== Front
bioRxiv
BIORXIV
bioRxiv
2692-8205
Cold Spring Harbor Laboratory

10.1101/2024.08.29.610280
preprint
1
Article
Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon
Hartley Gabrielle A. http://orcid.org/0000-0002-5672-2171

Okhovat Mariam
Hoyt Savannah J. http://orcid.org/0000-0001-7804-3236

Fuller Emily
Pauloski Nicole http://orcid.org/0009-0004-6135-7078

Alexandre Nicolas http://orcid.org/0000-0003-1530-1570

Alexandrov Ivan http://orcid.org/0000-0003-4342-2003

Drennan Ryan http://orcid.org/0009-0003-9918-1621

Dubocanin Danilo
Gilbert David M. http://orcid.org/0000-0001-8087-9737

Mao Yizi http://orcid.org/0000-0001-5743-6831

McCann Christine http://orcid.org/0009-0003-6256-4864

Neph Shane
Ryabov Fedor http://orcid.org/0000-0001-8728-9465

Sasaki Takayo http://orcid.org/0000-0001-7609-9316

Storer Jessica M.
Svendsen Derek
Troy William http://orcid.org/0000-0002-7906-0887

Wells Jackson http://orcid.org/0000-0002-4542-8604

Core Leighton http://orcid.org/0000-0002-1698-1144

Stergachis Andrew http://orcid.org/0000-0002-1299-3674

Carbone Lucia
O’Neill Rachel J. http://orcid.org/0000-0002-1525-6821

30 8 2024
2024.08.29.610280https://creativecommons.org/licenses/by-nc-nd/4.0/ This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
http://biorxiv.org/lookup/doi/10.1101/2024.08.29.610280
nihpp-2024.08.29.610280.pdf
Summary

Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here we characterize assembled centromeres in the Eastern hoolock gibbon, Hoolock leuconedys (HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence this epigenetic feature is conserved in the absence of satellite arrays; nevertheless, we report a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, large structural variations define HLE centromeres and distinguish them from other gibbons. Combined with differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, we propose that a “perfect storm” of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.
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