Evidence map›Paper›PMID 40088887›Full record

ArticleCell genomics2025

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

Gabrielle A Hartley, Mariam Okhovat, Savannah J Hoyt, Emily Fuller, Nicole Pauloski, Nicolas Alexandre, Ivan Alexandrov, Ryan Drennan, Danilo Dubocanin, David M Gilbert and 13 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

11 citing papers in PubMed.

  1. Article
  2. Review
  3. Review
  4. Article
  5. 40 years of CENP-A: the foundation of a new era of centromere biology.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2025
    Article
  6. Article
  7. Article
  8. A haplotype-resolved view of human gene regulation.bioRxiv : the preprint server for biology · 2025
    Article
  9. Article
  10. Article
  11. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

23 authors.

Gabrielle A HartleyInstitute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
Mariam OkhovatDepartment of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA.
Savannah J HoytInstitute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
Emily FullerInstitute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
Nicole PauloskiInstitute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
Nicolas AlexandreDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.
Ivan AlexandrovDepartment of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
Ryan DrennanInstitute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
Danilo DubocaninDivision of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
David M GilbertSan Diego Biomedical Research Institute, San Diego, CA 92121, USA.
Yizi MaoDivision of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
Christine McCannInstitute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
Shane NephDivision of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
Fedor RyabovUC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
Takayo SasakiSan Diego Biomedical Research Institute, San Diego, CA 92121, USA.
Jessica M StorerInstitute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
Derek SvendsenInstitute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
William TroyFormBio, Dallas, TX, USA.
Jackson WellsDepartment of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA.
Leighton CoreInstitute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
Andrew StergachisDivision of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
Lucia CarboneDepartment 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.
Rachel J O'NeillInstitute 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. Electronic address: rachel.oneill@uconn.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

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 fully 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 that this epigenetic feature is conserved in the absence of satellite arrays. We uncovered a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, we identify duplications and deletions in HLE centromeres that distinguish them from other gibbons. Finally, we observed differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, and thus propose that a combination of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.

Indexed as

CentromereDNA Transposable ElementsEpigenesis, GeneticHylobatesAnimalsCpG IslandsDNA MethylationEvolution, MolecularKaryotypeDNA Transposable Elementscentromereschromosome evolutiongenome assemblygibbonsmethylationprimate genomicsreplication timingtransposable elements

Identifiers

PMID40088887
PMCPMC12008813

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.