Evidence map›Paper›PMID 40138713›Full record

ArticleNucleic acids research2025

A dynamic structural unit of phase-separated heterochromatin protein 1α as revealed by integrative structural analyses.

Ayako Furukawa, Kento Yonezawa, Tatsuki Negami, Yuriko Yoshimura, Aki Hayashi, Jun-Ichi Nakayama, Naruhiko Adachi, Toshiya Senda, Kentaro Shimizu, Tohru Terada and 2 more

Abstract read
In one paragraph

Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

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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.

Ayako FurukawaGraduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Kento YonezawaStructural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.
Tatsuki NegamiDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
Yuriko YoshimuraDivision of Chromatin Regulation, National Institute for Basic Biology, Okazaki 444-8585, Japan.
Aki HayashiDivision of Chromatin Regulation, National Institute for Basic Biology, Okazaki 444-8585, Japan.
Jun-Ichi NakayamaDivision of Chromatin Regulation, National Institute for Basic Biology, Okazaki 444-8585, Japan.
Naruhiko AdachiStructural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.
Toshiya SendaStructural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.
Kentaro ShimizuDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
Tohru TeradaDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
Nobutaka ShimizuPhoton Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.
Yoshifumi NishimuraGraduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.ORCID 0000-0002-5148-3458

Funding

Grants-in-Aid for Scientific Research JPMXS0450100021Japan Agency for Medical Research and Development JP21am0101073,Japan Society for the Promotion of Science 21K06100Ministry of Education
6 · The paper itself

Abstract

The heterochromatin protein HP1α consists of an N-terminal disordered tail (N-tail), chromodomain (CD), hinge region (HR), and C-terminal chromo shadow domain (CSD). While CD binds to the lysine9-trimethylated histone H3 (H3K9me3) tail in nucleosomes, CSD forms a dimer bridging two nucleosomes with H3K9me3. Phosphorylation of serine residues in the N-tail enhances both H3K9me3 binding and liquid-liquid phase separation (LLPS) by HP1α. We have used integrative structural methods, including nuclear magnetic resonance, small-angle X-ray scattering (SAXS), and multi-angle-light scattering combined with size-exclusion chromatography, and coarse-grained molecular dynamics simulation with SAXS, to probe the HP1α dimer and its CSD deletion monomer. We show that dynamic intra- and intermolecular interactions between the N-tails and basic segments in CD and HR depend on N-tail phosphorylation. While the phosphorylated HP1α dimer undergoes LLPS via the formation of aggregated multimers, the N-tail phosphorylated mutant without CSD still undergoes LLPS, but its structural unit is a dynamic intermolecular dimer formed via the phosphorylated N-tail and a basic segment at the CD end. Furthermore, we reveal that mutation of this basic segment in HP1α affects the size of heterochromatin foci in cultured mammalian cells, suggesting that this interaction plays an important role in heterochromatin formation in vivo.

Indexed as

Chromosomal Proteins, Non-HistoneChromobox Protein Homolog 5HeterochromatinHistonesHumansMolecular Dynamics SimulationPhosphorylationProtein BindingProtein DomainsProtein MultimerizationScattering, Small AngleX-Ray DiffractionCBX5 protein, humanChromobox Protein Homolog 5Chromosomal Proteins, Non-HistoneHeterochromatinHistones

Identifiers

PMID40138713
PMCPMC11930357

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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.