Evidence map›Paper›PMID 38187757›Full record

ArticlebioRxiv : the preprint server for biology2023

CDCA7 is a hemimethylated DNA adaptor for the nucleosome remodeler HELLS.

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

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed, 2 citations in OpenAlex.

  1. Protein Multiple Conformation Prediction Using Multi-Objective Evolution Algorithm.Interdisciplinary sciences, computational life sciences · 2024
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

15 authors at 3 institutions in 2 countries.

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
Moeri HirutaStructural 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.
Reia ShikimachiStructural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan.
Amika KikuchiStructural 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.ORCID 0000-0002-6707-3584
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
Rockefeller University · USThe University of Tokyo · JPYokohama City University Medical Center · JP

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-facial anomalies (ICF) syndrome, characterized by hypomethylation at heterochromatin. The unique zinc-finger domain, zf-4CXXC_R1, of CDCA7 is widely conserved across eukaryotes but is absent from species that lack HELLS and DNA methyltransferases, implying its specialized relation with methylated DNA. Here we demonstrate that zf-4CXXC_R1 acts as a hemimethylated DNA sensor. The zf-4CXXC_R1 domain of CDCA7 selectively binds to DNA with a hemimethylated CpG, but not unmethylated or fully methylated CpG, and ICF disease mutations eliminated this binding. CDCA7 and HELLS interact via their N-terminal alpha helices, through which HELLS is recruited to hemimethylated DNA. While placement of a hemimethylated CpG within the nucleosome core particle can hinder its recognition by CDCA7, cryo-EM structure analysis of the CDCA7-nucleosome complex suggests that zf-4CXXC_R1 recognizes a hemimethylated CpG in the major groove at linker DNA. Our study provides insights into how the CDCA7-HELLS nucleosome remodeling complex uniquely assists maintenance DNA methylation.

Identifiers

PMID38187757
PMCPMC10769307
OpenAlexW4390012161

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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.