ArticleMolecular & cellular proteomics : MCP2013
The proteomic investigation of chromatin functional domains reveals novel synergisms among distinct heterochromatin components.
Article in Molecular & cellular proteomics : MCP, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- The Proteomic Composition and Organization of Constitutive Heterochromatin in Mouse Tissues.Cells · 2024Article
- Chemical Biology Approaches to Identify and Profile Interactors of Chromatin Modifications.ACS chemical biology · 2023Review
- Multi-layered chromatin proteomics identifies cell vulnerabilities in DNA repair.Nucleic acids research · 2023Article
- Interplay between chromatin marks in development and disease.Nature reviews. Genetics · 2022Review
- BAZ1B the Protean Protein.Genes · 2021Review
- Binding patterns of RNA-binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements.NAR genomics and bioinformatics · 2021Article
- Protein-DNA/RNA Interactions: An Overview of Investigation Methods in the -Omics Era.Journal of proteome research · 2021Review
- Review
- Native Chromatin Proteomics (N-ChroP) to Characterize Histone Post-translational Modification (PTM) Combinatorics at Distinct Genomic Regions.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Mass Spectrometry to Study Chromatin Compaction.Biology · 2020Review
- Targeting the scaffolding role of LSD1 (KDM1A) poises acute myeloid leukemia cells for retinoic acid-induced differentiation.Science advances · 2020Article
- Purification and enrichment of specific chromatin loci.Nature methods · 2020Review
- Expression and phase separation potential of heterochromatin proteins during early mouse development.EMBO reports · 2019Article
- All I's on the RADAR: role of ADAR in gene regulation.FEBS letters · 2018Review
- Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells.Journal of visualized experiments : JoVE · 2018Article
- Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes.Molecular cell · 2017Article
- Chromatin proteomics reveals novel combinatorial histone modification signatures that mark distinct subpopulations of macrophage enhancers.Nucleic acids research · 2017Article
- Mass Spectrometry-Based Tools to Characterize DNA-Protein Cross-Linking by Bis-Electrophiles.Basic & clinical pharmacology & toxicology · 2017Review
- Proteomics to study DNA-bound and chromatin-associated gene regulatory complexes.Human molecular genetics · 2016Article
- HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae.Genomics · 2016Article
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2 authors.
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Abstract
Chromatin is a highly dynamic, well-structured nucleoprotein complex of DNA and proteins that controls virtually all DNA transactions. Chromatin dynamicity is regulated at specific loci by the presence of various associated proteins, histones, post-translational modifications, histone variants, and DNA methylation. Until now the characterization of the proteomic component of chromatin domains has been held back by the challenge of enriching distinguishable, homogeneous regions for subsequent mass spectrometry analysis. Here we describe a modified protocol for chromatin immunoprecipitation combined with quantitative proteomics based on stable isotope labeling by amino acids in cell culture to identify known and novel histone modifications, variants, and complexes that specifically associate with silent and active chromatin domains. Our chromatin proteomics strategy revealed unique functional interactions among various chromatin modifiers, suggesting new regulatory pathways, such as a heterochromatin-specific modulation of DNA damage response involving H2A.X and WICH, both enriched in silent domains. Chromatin proteomics expands the arsenal of tools for deciphering how all the distinct protein components act together to enforce a given region-specific chromatin status.
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