Evidence map›Paper›PMID 41509222›Full record

ArticlebioRxiv : the preprint server for biology2025

Haplotype-Resolved Genomics Reveals Conserved Chromatin Architecture and Epigenetic Constraints of Human Neocentromeres.

Savannah J Hoyt, Gabrielle A Hartley, Mariah C Antopia, Thomas W Tullius, Dylan J Taylor, Nicole M Tillquist, Shane Neph, Nicole Pauloski, Katherine M Munson, Kendra Hoekzema and 4 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Savannah J HoytInstitute for Systems Genomics, University of Connecticut, Storrs, CT, USA.ORCID 0000-0001-7804-3236
Gabrielle A HartleyInstitute for Systems Genomics, University of Connecticut, Storrs, CT, USA.ORCID 0000-0002-5672-2171
Mariah C AntopiaDepartment of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID 0000-0002-9095-9009
Thomas W TulliusLewis-Sigler Institute, Princeton University, Princeton, NJ, USA.ORCID 0000-0002-4949-1440
Dylan J TaylorDepartment of Biology, Johns Hopkins University, Baltimore, MD, USA.ORCID 0000-0001-5806-4494
Nicole M TillquistInstitute for Systems Genomics, University of Connecticut, Storrs, CT, USA.ORCID 0000-0001-8596-5335
Shane NephDivision of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.ORCID 0000-0003-2962-8777
Nicole PauloskiInstitute for Systems Genomics, University of Connecticut, Storrs, CT, USA.ORCID 0009-0004-6135-7078
Katherine M MunsonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0001-8413-6498
Kendra HoekzemaDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0002-8058-0177
Evan E EichlerDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0002-8246-4014
Andrew B StergachisDivision of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.ORCID 0000-0002-1299-3674
Glennis A LogsdonDepartment of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID 0000-0003-2396-0656
Rachel J O'NeillInstitute for Systems Genomics, University of Connecticut, Storrs, CT, USA.ORCID 0000-0002-1525-6821

Funding

Sequence-resolved structural variation of human genomesR01HG010169 · NHGRI · UNIVERSITY OF WASHINGTON · PI Evan Eichler · 2018 to 2026
$4.5M
Function and fitness consequences of human genetic variationR35GM133747 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Rajiv Champion McCoy · 2019 to 2026
$3.3M
Investigating the contribution of non-coding genetic variation to rare disordersDP5OD029630 · OD · UNIVERSITY OF WASHINGTON · PI STERGACHIS, ANDREW BEN · 2020 to 2024
$1.9M
The Role of Retroelements in Centromere FunctionR01GM123312 · NIGMS · UNIVERSITY OF CONNECTICUT STORRS · PI O'NEILL, RACHEL · 2019 to 2022
$1.9M
Tooling for accurately studying the epigenome along the human pangenome referenceU01HG013744 · NHGRI · UNIVERSITY OF WASHINGTON · PI STERGACHIS, ANDREW BEN · 2024 to 2024
$1.4M
Human centromere variation and functionR00GM147352 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI Glennis Amelia Logsdon · 2024 to 2026
$747k
Uncovering sources of human gene expression variation in a globally diverse cohortF31HG012900 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI TAYLOR, DYLAN JAMES · 2023 to 2024
$97k
NHGRI NIH HHS F31 HG012900NHGRI NIH HHS R01 HG010169NHGRI NIH HHS U01 HG013744NIGMS NIH HHS R00 GM147352NIGMS NIH HHS R01 GM123312NIGMS NIH HHS R35 GM133747NIH HHS DP5 OD029630
6 · The paper itself

Abstract

Human neocentromeres are functional centromeres demarcated by CENP-A nucleosomes that form ectopically at alpha satellite-free loci. How neocentromeres reshape local chromatin and which features of native centromeric chromatin are preserved are unknown. We generated gapless, haplotype-resolved assemblies of native and neocentromeres from three patient-derived cell lines. Integrating CpG methylation, CENP-A profiling, and single-molecule chromatin fiber sequencing, we reveal chromatin features that define the essential centromeric architecture reconstituted during neocentromere establishment. We find that a deletion within the satellite array encompassing the hypo-CpG methylation centromere dip regions (CDRs) led to native centromere inactivation, that neocentromeres harbor CDRs and a dichromatin architecture, recapitulating features of alpha-satellite centromeres, and that LINEs demarcate neocentromere boundaries, implicating transposable elements in restricting CENP-A domain spreading. Moreover, neocentromeric chromatin is incompatible with promoter-like chromatin states, redefining the regulatory landscape within genic regions. Finally, using haplotype-specific chromatin footprinting, we resolve CENP-A nucleosome chromatin architecture of active centromeres.

Indexed as

CDRCENP-A nucleosomesCentromerechromatin accessibilityfiber-seqhaplotype-phased genome assemblyneocentromere

Identifiers

PMID41509222
PMCPMC12776110

What OpenQuestion holds

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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.