ArticleHuman molecular genetics2016
Proteomics to study DNA-bound and chromatin-associated gene regulatory complexes.
Article in Human molecular genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 1 of them a synthesis that pooled it.
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Who cites it
43 citing papers in PubMed, 1 synthesis or guideline pooled it, 71 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
- Site-specific programming characterizes dynamic post-translational acetylation of histone H2B lysine 108 in mouse embryonic stem cells.Nature communications · 2026Article
- CLOCK/BMAL1 interactome uncovers homeodomain factors as tissue regulators.Nature cell biology · 2026Article
- qChIP-MS reveals the local chromatin composition by label-free quantitative proteomics.Nature communications · 2026Article
- Methods for the Investigation of Protein-Ligands Interactions.Advances in experimental medicine and biology · 2026Review
- SP140 represses specific loci by recruiting polycomb repressive complex 2 and NuRD complex.Nucleic acids research · 2025Article
- Locus-specific proteome decoding reveals Fpt1 as a chromatin-associated negative regulator of RNA polymerase III assembly.Molecular cell · 2023Article
- Review
- Spatiotemporal and global profiling of DNA-protein interactions enables discovery of low-affinity transcription factors.Nature chemistry · 2023Article
- Binding and Kinetic Analysis of Human Protein Phosphatase PP2A Interactions with Caspase 9 Protein and the Interfering Peptide C9h.Pharmaceutics · 2022Article
- A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution.Nature ecology & evolution · 2022Article
- Chromatin Immunoprecipitation Assays on Medulloblastoma Cell Line DAOY.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Current Analytical Strategies in Studying Chromatin-Associated-Proteome (Chromatome).Molecules (Basel, Switzerland) · 2021Review
- Quantifying the phase separation property of chromatin-associated proteins under physiological conditions using an anti-1,6-hexanediol index.Genome biology · 2021Article
- Protein-DNA/RNA Interactions: An Overview of Investigation Methods in the -Omics Era.Journal of proteome research · 2021Review
- Integration of Data from Liquid-Liquid Phase Separation Databases Highlights Concentration and Dosage Sensitivity of LLPS Drivers.International journal of molecular sciences · 2021Article
- Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia.Nature methods · 2021Article
- Isolating and Analyzing Protein Containing Granules from Cells.Current protocols · 2021Article
- Transcriptional Enhancers inGenetics · 2020Review
- Mass spectrometry-based proteomic capture of proteins bound to the MACC1 promoter in colon cancer.Clinical & experimental metastasis · 2020Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-resolution mass spectrometry (MS)-based proteomics is a powerful method for the identification of soluble protein complexes and large-scale affinity purification screens can decode entire protein interaction networks. In contrast, protein complexes residing on chromatin have been much more challenging, because they are difficult to purify and often of very low abundance. However, this is changing due to recent methodological and technological advances in proteomics. Proteins interacting with chromatin marks can directly be identified by pulldowns with synthesized histone tails containing posttranslational modifications (PTMs). Similarly, pulldowns with DNA baits harbouring single nucleotide polymorphisms or DNA modifications reveal the impact of those DNA alterations on the recruitment of transcription factors. Accurate quantitation - either isotope-based or label free - unambiguously pinpoints proteins that are significantly enriched over control pulldowns. In addition, protocols that combine classical chromatin immunoprecipitation (ChIP) methods with mass spectrometry (ChIP-MS) target gene regulatory complexes in their in-vivo context. Similar to classical ChIP, cells are crosslinked with formaldehyde and chromatin sheared by sonication or nuclease digested. ChIP-MS baits can be proteins in tagged or endogenous form, histone PTMs, or lncRNAs. Locus-specific ChIP-MS methods would allow direct purification of a single genomic locus and the proteins associated with it. There, loci can be targeted either by artificial DNA-binding sites and corresponding binding proteins or via proteins with sequence specificity such as TAL or nuclease deficient Cas9 in combination with a specific guide RNA. We predict that advances in MS technology will soon make such approaches generally applicable tools in epigenetics.
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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.