Evidence map›Paper›PMID 40637225›Full record

ArticleNucleic acids research2025

Molecular determinants for recognition of serotonylated chromatin.

Laura Pulido-Cortés, Hajo Gielingh, Vito Thijssen, Minglong Liu, Ryoji Yoshisada, Leonardo Romão Soares, Sheikh Nizamuddin, Florian Friedrich, Holger Greschik, Ling Peng and 8 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 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Quinone reductase 2bioRxiv : the preprint server for biology · 2026
    Article
  3. Review
  4. 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

18 authors.

Laura Pulido-CortésGerman Cancer Consortium (DKTK), partner site Freiburg, a partnership between the DKFZ and Medical Center-University of Freiburg and Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany.
Hajo GielinghNMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands.
Vito ThijssenDepartment of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands.
Minglong LiuDepartment of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands.
Ryoji YoshisadaDepartment of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands.
Leonardo Romão SoaresDepartment of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands.
Sheikh NizamuddinGerman Cancer Consortium (DKTK), partner site Freiburg, a partnership between the DKFZ and Medical Center-University of Freiburg and Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany.ORCID 0000-0002-4586-5898
Florian FriedrichInstitute of Pharmaceutical Sciences, University of Freiburg, 79104 Freiburg, Germany.ORCID 0000-0001-5420-6184
Holger GreschikGerman Cancer Consortium (DKTK), partner site Freiburg, a partnership between the DKFZ and Medical Center-University of Freiburg and Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany.
Ling PengGerman Cancer Consortium (DKTK), partner site Freiburg, a partnership between the DKFZ and Medical Center-University of Freiburg and Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany.
Rodrigo Vargas HonoratoNMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands.
Manfred JungInstitute of Pharmaceutical Sciences, University of Freiburg, 79104 Freiburg, Germany.
Alexandre M J J BonvinNMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands.ORCID 0000-0001-7369-1322
Martin L BiniossekInstitute of Molecular Medicine and Cell Research, Medical Center-University of Freiburg, 79016 Freiburg, Germany.
Roland SchüleGerman Cancer Consortium (DKTK), partner site Freiburg, a partnership between the DKFZ and Medical Center-University of Freiburg and Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany.
Seino JongkeesDepartment of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands.
Hugo van IngenNMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands.ORCID 0000-0002-0808-3811
H Th Marc TimmersGerman Cancer Consortium (DKTK), partner site Freiburg, a partnership between the DKFZ and Medical Center-University of Freiburg and Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany.ORCID 0000-0001-7062-1417

Funding

Deutsche Forschungsgemeinschaft 503267011Deutsche Forschungsgemeinschaft Ju295/18-1Deutsche Forschungsgemeinschaft SFB992Deutsche Forschungsgemeinschaft TI688/1-1Deutsche Konsortium für Translationale KrebsforschungDutch Research Council 17437European High Performance Computing Joint Undertaking 101093290European High Performance Computing Joint Undertaking 823830European High Performance Computing Joint Undertaking BioExceliNEXT-Discovery PID 12004Utrecht University
6 · The paper itself

Abstract

Post-translational modifications of histone tails constitute a key epigenetic mechanism controlling chromatin environment and gene transcription. Serotonylation of histone H3Q5 (H3Q5ser) is a recently discovered mark associated with active transcription of RNA polymerase II (pol II)-transcribed genes. The direct link between H3Q5ser and the pol II transcription machinery relies on the TFIID subunit TAF3. The presence of H3Q5ser enhances TAF3 binding to H3K4me3, but the molecular determinants underlying this interaction remained unclear. Here, we resolve the binding mode of TAF3-PHD to H3K4me3Q5ser identifying a novel binding surface for H3Q5ser using solution nuclear magnetic resonance spectroscopy. This reveals how H3Q5ser recognizes a conserved surface of the TAF3-PHD via CH-π interactions in an edge-face conformation involving a proline residue stabilized by a tryptophan. This combination of proline and tryptophan is unique to the PHD finger of TAF3 and conserved among TAF3 orthologues. Our findings establish a framework for the molecular recognition of serotonylated chromatin, laying the foundation for developing epigenetic inhibitors targeting serotonylation-dependent transcriptional regulation in neuronal development.

Indexed as

ChromatinHistonesTATA-Binding Protein Associated FactorsTranscription Factor TFIIDBinding SitesEpigenesis, GeneticHistone AcetyltransferasesHumansModels, MolecularProtein BindingProtein Processing, Post-TranslationalRNA Polymerase IIChromatinHistone AcetyltransferasesHistonesRNA Polymerase IITATA-binding protein associated factor 250 kDaTATA-Binding Protein Associated FactorsTranscription Factor TFIID

Identifiers

PMID40637225
PMCPMC12238850

What OpenQuestion holds

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LicenceCC BY
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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.