Evidence map›Paper›PMID 34782608›Full record

ArticleNature communications2021

Structural basis of the regulation of the normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2.

Ko Sato, Amarjeet Kumar, Keisuke Hamada, Chikako Okada, Asako Oguni, Ayumi Machiyama, Shun Sakuraba, Tomohiro Nishizawa, Osamu Nureki, Hidetoshi Kono and 2 more

Open access · goldAbstract read
In one paragraph

Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.

0numbers the graph read from it
0cells of the map it votes in
25citing papers in PubMed
2.8field-weighted citation impact, top 8% of its field
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

25 citing papers in PubMed, 41 citations in OpenAlex.

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  20. Histone Maps inInternational journal of molecular sciences · 2023
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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

12 authors at 3 institutions in 1 country.

Ko Sato *Department of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan.
Amarjeet KumarInstitute for Quantum Life Science, National Institutes for Quantum Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan.ORCID http://orcid.org/0000-0001-7740-9881
Keisuke HamadaDepartment of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan.
Chikako OkadaDepartment of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan.
Asako OguniDepartment of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan.
Ayumi MachiyamaDepartment of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan.
Shun SakurabaInstitute for Quantum Life Science, National Institutes for Quantum Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan.ORCID http://orcid.org/0000-0001-5768-2389
Tomohiro NishizawaDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.ORCID http://orcid.org/0000-0001-7463-8398
Osamu NurekiDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.ORCID http://orcid.org/0000-0003-1813-7008
Hidetoshi KonoInstitute for Quantum Life Science, National Institutes for Quantum Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan.ORCID http://orcid.org/0000-0001-5729-8707
Kazuhiro OgataDepartment of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan. ogata@yokohama-cu.ac.jp.
Toru Sengoku *Department of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan. tsengoku@yokohama-cu.ac.jp.ORCID http://orcid.org/0000-0001-9461-8714
Yokohama City University · JPNational Institutes for Quantum Science and Technology · JPThe University of Tokyo · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Dimethylated histone H3 Lys36 (H3K36me2) regulates gene expression, and aberrant H3K36me2 upregulation, resulting from either the overexpression or point mutation of the dimethyltransferase NSD2, is found in various cancers. Here we report the cryo-electron microscopy structure of NSD2 bound to the nucleosome. Nucleosomal DNA is partially unwrapped, facilitating NSD2 access to H3K36. NSD2 interacts with DNA and H2A along with H3. The NSD2 autoinhibitory loop changes its conformation upon nucleosome binding to accommodate H3 in its substrate-binding cleft. Kinetic analysis revealed that two oncogenic mutations, E1099K and T1150A, increase NSD2 catalytic turnover. Molecular dynamics simulations suggested that in both mutants, the autoinhibitory loop adopts an open state that can accommodate H3 more often than the wild-type. We propose that E1099K and T1150A destabilize the interactions that keep the autoinhibitory loop closed, thereby enhancing catalytic turnover. Our analyses guide the development of specific inhibitors of NSD2.

Indexed as

DNA MethylationCarcinogenesisCryoelectron MicroscopyEpigenomicsHistone-Lysine N-MethyltransferaseHistonesHumansKineticsMethylationMolecular Dynamics SimulationNeoplasmsOncogenesRepressor ProteinsHistone-Lysine N-MethyltransferaseHistonesNSD2 protein, humanRepressor Proteins

Identifiers

PMID34782608
PMCPMC8593083
OpenAlexW3213084863

What OpenQuestion holds

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LicenceCC BY
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.