Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.

Autor:	Hartley GA; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Okhovat M; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA., Hoyt SJ; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Fuller E; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Pauloski N; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Alexandre N; Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA., Alexandrov I; Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Israel., Drennan R; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Dubocanin D; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA., Gilbert DM; San Diego Biomedical Research Institute, San Diego, CA 92121, USA., Mao Y; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA., McCann C; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Neph S; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA., Ryabov F; UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA.; Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA., Sasaki T; San Diego Biomedical Research Institute, San Diego, CA 92121, USA., Storer JM; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Svendsen D; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Troy W; FormBio, Dallas, TX, USA., Wells J; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA., Core L; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Stergachis A; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA., Carbone L; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA.; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA.; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA.; Division of Genetics, Oregon National Primate Research Center, Portland, OR, USA., O'Neill RJ; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA.
Jazyk:	angličtina
Zdroj:	BioRxiv : the preprint server for biology [bioRxiv] 2024 Aug 30. Date of Electronic Publication: 2024 Aug 30.
DOI:	10.1101/2024.08.29.610280
Abstrakt:	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. Competing Interests: Declaration of Interests R.J.O. serves on the SAB of Colossal Biosciences and has been supported to present at ONT events.
Databáze:	MEDLINE
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