Evidence map›Paper›PMID 39762271›Full record

ArticleNature communications2025

Development of nucleus-targeted histone-tail-based photoaffinity probes to profile the epigenetic interactome in native cells.

Yu Wang, Jian Fan, Xianbin Meng, Qingyao Shu, Yincui Wu, Guo-Chao Chu, Rong Ji, Yinshan Ye, Xiangwei Wu, Jing Shi and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed, 1 pooled it
–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

11 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
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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

13 authors.

Yu Wang *School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Key Laboratory of Animal Source of Anhui Province, Hefei University of Technology, Hefei, 230009, China.
Jian Fan *Department of Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, 230026, China.
Xianbin Meng *MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
Qingyao Shu *Department of Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, 230026, China.
Yincui WuSchool of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Key Laboratory of Animal Source of Anhui Province, Hefei University of Technology, Hefei, 230009, China.
Guo-Chao ChuNew Cornerstone Science Laboratory, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China. cgc.2020@tsinghua.org.cn.ORCID http://orcid.org/0000-0003-2785-3399
Rong JiSchool of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Key Laboratory of Animal Source of Anhui Province, Hefei University of Technology, Hefei, 230009, China.
Yinshan YeSchool of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Key Laboratory of Animal Source of Anhui Province, Hefei University of Technology, Hefei, 230009, China.
Xiangwei WuNew Cornerstone Science Laboratory, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China.ORCID http://orcid.org/0009-0002-9367-8306
Jing ShiDepartment of Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, 230026, China.
Haiteng DengMOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.ORCID http://orcid.org/0000-0001-9496-1280
Lei LiuNew Cornerstone Science Laboratory, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China. lliu@mail.tsinghua.edu.cn.ORCID http://orcid.org/0000-0001-6290-8602
Yi-Ming LiSchool of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Key Laboratory of Animal Source of Anhui Province, Hefei University of Technology, Hefei, 230009, China. ymli@hfut.edu.cn.ORCID http://orcid.org/0000-0001-6716-8199

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Dissection of the physiological interactomes of histone post-translational modifications (hPTMs) is crucial for understanding epigenetic regulatory pathways. Peptide- or protein-based histone photoaffinity tools expanded the ability to probe the epigenetic interactome, but in situ profiling in native cells remains challenging. Here, we develop a nucleus-targeting histone-tail-based photoaffinity probe capable of profiling the hPTM-mediated interactomes in native cells, by integrating cell-permeable and nuclear localization peptide modules into an hPTM peptide equipped with a photoreactive moiety. These types of probes, such as histone H3 lysine 4 trimethylation and histone H3 Lysine 9 crotonylation probes, enable the probing of epigenetic interactomes both in HeLa cell and hard-to-transfect RAW264.7 cells, resulting in the discovery of distinct interactors in different cell lines. The utility of this probe is further exemplified by characterizing interactome of emerging hPTM, such as AF9 was detected as a binder of histone H3 Lysine 9 lactylation, thus expanding the toolbox for profiling of hPTM-mediated PPIs in live cells.

Indexed as

Cell NucleusEpigenesis, GeneticHistonesProtein Processing, Post-TranslationalAnimalsHeLa CellsHumansLysineMethylationMicePeptidesPhotoaffinity LabelsRAW 264.7 Cellshistone H3 trimethyl Lys4HistonesLysinePeptidesPhotoaffinity Labels

Identifiers

PMID39762271
PMCPMC11704063

What OpenQuestion holds

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LicenceCC BY-NC-ND
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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.