Evidence map›Paper›PMID 39178260›Full record

ArticleScience advances2024

CDCA7 is an evolutionarily conserved hemimethylated DNA sensor in eukaryotes.

Isabel E Wassing, Atsuya Nishiyama, Reia Shikimachi, Qingyuan Jia, Amika Kikuchi, Moeri Hiruta, Keita Sugimura, Xin Hong, Yoshie Chiba, Junhui Peng and 5 more

Abstract read
In one paragraph

Article in Science advances, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.

0numbers the graph read from it
0cells of the map it votes in
20citing 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

20 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Oncology research · 2026
    Article
  6. Review
  7. Reconstitution of genome remodeling usingFrontiers in cell and developmental biology · 2026
    Review
  8. CDCA7 facilitates MET1-mediated CG DNA methylation maintenance in centromeric heterochromatin via linker histone H1.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  9. Article
  10. Article
  11. Article
  12. Sustainable integrative cell biology: CENP-C is guilty by association.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2025
    Article
  13. IMPACTS OF DNA METHYLATION ON H2A.Z DEPOSITION AND NUCLEOSOME STABILITY.bioRxiv : the preprint server for biology · 2025
    Article
  14. Article
  15. SCoTCH-seq reveals that 5-hydroxymethylcytosine encodes regulatory information across DNA strands.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  16. Article
  17. Review
  18. Cellular senescence as a source of chronic microinflammation that promotes the aging process.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2025
    Review
  19. Article
  20. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

15 authors.

Isabel E WassingLaboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA.ORCID 0000-0001-5937-7273
Atsuya NishiyamaDivision of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Tokyo 108-8639, Japan.ORCID 0000-0002-8416-3776
Reia ShikimachiStructural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan.
Qingyuan JiaLaboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA.ORCID 0009-0008-8030-7198
Amika KikuchiStructural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan.ORCID 0000-0002-5112-0868
Moeri HirutaStructural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan.
Keita SugimuraDivision of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Tokyo 108-8639, Japan.
Xin HongDivision of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Tokyo 108-8639, Japan.
Yoshie ChibaDivision of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Tokyo 108-8639, Japan.
Junhui PengLaboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA.ORCID 0000-0003-2855-2299
Christopher JennessLaboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA.
Makoto NakanishiDivision of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Tokyo 108-8639, Japan.
Li ZhaoLaboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA.ORCID 0000-0001-6776-1996
Kyohei AritaStructural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan.ORCID 0000-0002-9762-8405
Hironori FunabikiLaboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA.ORCID 0000-0003-4831-4087

Funding

Regulation of mitotic chromosomes - Revision - 2R35GM132111 · NIGMS · ROCKEFELLER UNIVERSITY · PI Hironori Funabiki · 2019 to 2026
$6.9M
The genetic and epigenetic mechanisms of phenotypic innovationhttps://apps.era.nih.gov/gm/reportCheckList.do?applicationID=9798249R35GM133780 · NIGMS · ROCKEFELLER UNIVERSITY · PI Li Zhao · 2019 to 2026
$3.5M
NIGMS NIH HHS R35 GM132111NIGMS NIH HHS R35 GM133780
6 · The paper itself

Abstract

Mutations of the SNF2 family ATPase HELLS and its activator CDCA7 cause immunodeficiency, centromeric instability, and facial anomalies syndrome, characterized by DNA hypomethylation at heterochromatin. It remains unclear why CDCA7-HELLS is the sole nucleosome remodeling complex whose deficiency abrogates the maintenance of DNA methylation. We here identify the unique zinc-finger domain of CDCA7 as an evolutionarily conserved hemimethylation-sensing zinc finger (HMZF) domain. Cryo-electron microscopy structural analysis of the CDCA7-nucleosome complex reveals that the HMZF domain can recognize hemimethylated CpG in the outward-facing DNA major groove within the nucleosome core particle, whereas UHRF1, the critical activator of the maintenance methyltransferase DNMT1, cannot. CDCA7 recruits HELLS to hemimethylated chromatin and facilitates UHRF1-mediated H3 ubiquitylation associated with replication-uncoupled maintenance DNA methylation. We propose that the CDCA7-HELLS nucleosome remodeling complex assists the maintenance of DNA methylation on chromatin by sensing hemimethylated CpG that is otherwise inaccessible to UHRF1 and DNMT1.

Indexed as

CCAAT-Enhancer-Binding ProteinsDNA MethylationNucleosomesUbiquitin-Protein LigasesAdenosine TriphosphatasesCell Cycle ProteinsChromatinCpG IslandsCryoelectron MicroscopyDNADNA (Cytosine-5-)-Methyltransferase 1DNA HelicasesEukaryotaEvolution, MolecularHistonesHumansAdenosine TriphosphatasesCCAAT-Enhancer-Binding ProteinsCDCA7 protein, humanCell Cycle ProteinsChromatinDNADNA (Cytosine-5-)-Methyltransferase 1DNA HelicasesHELLS protein, humanHistonesNuclear ProteinsNucleosomesUbiquitin-Protein LigasesUHRF1 protein, human

Identifiers

PMID39178260
PMCPMC11343034

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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.