ArticleThe EMBO journal2014
Proteomics of a fuzzy organelle: interphase chromatin.
Article in The EMBO journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 1 of them a synthesis that pooled it.
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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.
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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.
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Who cites it
37 citing papers in PubMed, 1 synthesis or guideline pooled it, 78 citations in OpenAlex.
- (Re)defining the human chromatome: an integrated meta-analysis of localization, function, abundance, physical properties, and domain composition of chromatin proteins.Nucleic acids research · 2026Pooled it
- Quantitative proteomics reveals coordinated changes in the proteome during replicative senescence.Nature communications · 2026Article
- Rules of engagement for condensins and cohesins guide mitotic chromosome formation.Science (New York, N.Y.) · 2025Article
- DNA damage-induced proteasome phosphorylation controls substrate recognition and facilitates DNA repair.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Rules of engagement for condensins and cohesins guide mitotic chromosome formation.bioRxiv : the preprint server for biology · 2024Article
- Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction.Nature communications · 2024Article
- The antiproliferative effect of FGF2 in K-Ras-driven tumor cells involves modulation of rRNA and the nucleolus.Journal of cell science · 2023Article
- DNA mimic foldamers affect chromatin composition and disturb cell cycle progression.Nucleic acids research · 2023Article
- Investigating phase separation properties of chromatin-associated proteins using gradient elution of 1,6-hexanediol.BMC genomics · 2023Article
- Higher-order modular regulation of the human proteome.Molecular systems biology · 2023Article
- Comprehensive chromatin proteomics resolves functional phases of pluripotency and identifies changes in regulatory components.Nucleic acids research · 2023Article
- Chromatin Enrichment for Proteomics in Plants (ChEP-P).Methods in molecular biology (Clifton, N.J.) · 2023Article
- PARP1 proximity proteomics reveals interaction partners at stressed replication forks.Nucleic acids research · 2022Article
- Understudied proteins: opportunities and challenges for functional proteomics.Nature methods · 2022Article
- Mapping the invisible chromatin transactions of prophase chromosome remodeling.Molecular cell · 2022Article
- Subcellular Transcriptomics and Proteomics: A Comparative Methods Review.Molecular & cellular proteomics : MCP · 2022Review
- Current Analytical Strategies in Studying Chromatin-Associated-Proteome (Chromatome).Molecules (Basel, Switzerland) · 2021Review
- Proteome dynamics at broken replication forks reveal a distinct ATM-directed repair response suppressing DNA double-strand break ubiquitination.Molecular cell · 2021Article
- Tools for Decoding Ubiquitin Signaling in DNA Repair.Frontiers in cell and developmental biology · 2021Review
- The chromatin bound proteome of the human malaria parasite.Microbial genomics · 2020Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
Abstract
Chromatin proteins mediate replication, regulate expression, and ensure integrity of the genome. So far, a comprehensive inventory of interphase chromatin has not been determined. This is largely due to its heterogeneous and dynamic composition, which makes conclusive biochemical purification difficult, if not impossible. As a fuzzy organelle, it defies classical organellar proteomics and cannot be described by a single and ultimate list of protein components. Instead, we propose a new approach that provides a quantitative assessment of a protein's probability to function in chromatin. We integrate chromatin composition over a range of different biochemical and biological conditions. This resulted in interphase chromatin probabilities for 7635 human proteins, including 1840 previously uncharacterized proteins. We demonstrate the power of our large-scale data-driven annotation during the analysis of cyclin-dependent kinase (CDK) regulation in chromatin. Quantitative protein ontologies may provide a general alternative to list-based investigations of organelles and complement Gene Ontology.
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What OpenQuestion holds
Registered trials
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.