Evidence map›Paper›PMID 39142653›Full record

ArticleNucleic acids research2024

The C-terminal 4CXXC-type zinc finger domain of CDCA7 recognizes hemimethylated DNA and modulates activities of chromatin remodeling enzyme HELLS.

Akeo Shinkai, Hideharu Hashimoto, Chikako Shimura, Hiroaki Fujimoto, Kei Fukuda, Naoki Horikoshi, Masaki Okano, Hitoshi Niwa, Erik W Debler, Hitoshi Kurumizaka and 1 more

Abstract read
In one paragraph

Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing 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

14 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Article
  6. Review
  7. Oncology research · 2026
    Article
  8. Review
  9. 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
  10. Article
  11. Article
  12. Article
  13. 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
  14. Article
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

11 authors.

Akeo ShinkaiCellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako City, Saitama 351-0198, Japan.
Hideharu HashimotoDepartment of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
Chikako ShimuraCellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako City, Saitama 351-0198, Japan.
Hiroaki FujimotoCellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako City, Saitama 351-0198, Japan.
Kei FukudaFaculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi 400-8510, Japan.
Naoki HorikoshiLaboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.ORCID 0000-0003-1842-6934
Masaki OkanoDepartment of Pluripotent Stem Cell Biology, IMEG, Kumamoto university, Honjo 2-2-1, Chuo-ku, Kumamoto, Kumamoto 860-0811, Japan.
Hitoshi NiwaDepartment of Pluripotent Stem Cell Biology, IMEG, Kumamoto university, Honjo 2-2-1, Chuo-ku, Kumamoto, Kumamoto 860-0811, Japan.
Erik W DeblerDepartment of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA.ORCID 0000-0002-2587-2150
Hitoshi KurumizakaLaboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.ORCID 0000-0001-7412-3722
Yoichi ShinkaiCellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako City, Saitama 351-0198, Japan.ORCID 0000-0002-6051-2484

Funding

Chromatin Biology of the African TrypanosomeR01AI165840 · NIAID · THOMAS JEFFERSON UNIVERSITY · PI DEBLER, ERIK · 2022 to 2025
$2.8M
AMED JP23ama121009Japan Ministry of Education, Culture, Sports, Science and Technology Grant-in-Aid for Scientific Research 18H05530Japan Science and Technology Agency JPMJER1901Japan Society for the Promotion of ScienceNational Institute of Allergy and Infectious DiseasesNIAID NIH HHS R01 AI165840NIH HHS R01 AI165840Research Support Project for Life Science and Drug DiscoveryRIKEN
6 · The paper itself

Abstract

The chromatin-remodeling enzyme helicase lymphoid-specific (HELLS) interacts with cell division cycle-associated 7 (CDCA7) on nucleosomes and is involved in the regulation of DNA methylation in higher organisms. Mutations in these genes cause immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome, which also results in DNA hypomethylation of satellite repeat regions. We investigated the functional domains of human CDCA7 in HELLS using several mutant CDCA7 proteins. The central region is critical for binding to HELLS, activation of ATPase, and nucleosome sliding activities of HELLS-CDCA7. The N-terminal region tends to inhibit ATPase activity. The C-terminal 4CXXC-type zinc finger domain contributes to CpG and hemimethylated CpG DNA preference for DNA-dependent HELLS-CDCA7 ATPase activity. Furthermore, CDCA7 showed a binding preference to DNA containing hemimethylated CpG, and replication-dependent pericentromeric heterochromatin foci formation of CDCA7 with HELLS was observed in mouse embryonic stem cells; however, all these phenotypes were lost in the case of an ICF syndrome mutant of CDCA7 mutated in the zinc finger domain. Thus, CDCA7 most likely plays a role in the recruitment of HELLS, activates its chromatin remodeling function, and efficiently induces DNA methylation, especially at hemimethylated replication sites.

Indexed as

Chromatin Assembly and DisassemblyDNA HelicasesDNA MethylationZinc FingersAdenosine TriphosphatasesAnimalsCell Cycle ProteinsCpG IslandsDNAFaceHeterochromatinHumansImmunologic Deficiency SyndromesMiceMouse Embryonic Stem CellsMutationAdenosine TriphosphatasesCDCA7 protein, humanCell Cycle ProteinsDNADNA HelicasesHELLS protein, humanHeterochromatinNuclear ProteinsNucleosomes

Identifiers

PMID39142653
PMCPMC11417364

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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.