A map of general and specialized chromatin readers in mouse tissues generated by label-free interaction proteomics
Open accessAbstract
Posttranslational modifications on core histones can serve as binding scaffolds for chromatin-associated proteins. Proteins that specifically bind to or "read" these modifications were previously identified in mass spectrometry-based proteomics screens based on stable isotope-labeling in cell lines. Here we describe a sensitive, label-free histone peptide pull-down technology with extracts of different mouse tissues. Applying this workflow to the classical activating and repressive epigenetic marks on histone H3, H3K4me3, and H3K9me3, we identified known and putative readers in extracts from brain, liver, kidney, and testis. A large class of proteins were specifically repelled by H3K4me3. Our screen reached near-saturation of direct interactors, most of which are ubiquitously expressed. In addition, it revealed a number of specialized readers in tissues such as testis. Apart from defining the chromatin interaction landscape in mouse tissues, our workflow can be used for peptides with different modifications and cell types of any organism.
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GFP-MBD3 affinity purification identified known NuRD core subunits and previously described interactors ZMYND8, ZNF592, and SALL4.
“In each of these pulldowns, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were detected, including ZMYND8, ZNF592, and SALL4 [8,14,17].”
MaxLFQ is capable of achieving quantification accuracies comparable to SILAC in interaction proteomics cases.
“We have recently shown that both SILAC and MaxLFQ generate similar ratio distributions (57), indicating that in such cases MaxLFQ is capable of achieving quantification accuracies comparable to those obtained with SILAC.”
From Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ (2014) · cites this paper as [57]
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References 49 · Cited by 189
- Authors
- Eberl, H. C., Spruijt, C. G., Kelstrup, C. D., Vermeulen, M., & Mann, M.
- Affiliations
- Max Planck Institute of Biochemistry (DE)
- University Medical Center Utrecht (NL)
- University of Copenhagen (DK)
- Corresponding author
- Vermeulen, Michiel
- Mann, Matthias
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2013-01
- Volume
- 49
- Issue
- 2
- Pages
- 368-378
- ISSN
- 1097-2765 (ISSN-L)
- OpenAlex
- W2087543106
- Cited by
- 189
- References
- 49
- Citations by year
- 2026: 1 · 2025: 7 · 2024: 12 · 2023: 10 · 2022: 15 · 2021: 20 · 2020: 13 · 2019: 14 · 2018: 15 · 2017: 18 · 2016: 17 · 2015: 19 · 2014: 17 · 2013: 11
- FWCI
- 6.05
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Keywords
- chromatin reader, histone modifications, histone H3, H3K4me3, H3K9me3, epigenetic modifications, chromatin proteins, mouse tissues, testis, brain, liver, kidney, protein-protein interaction
- MeSH terms
- Animals, Brain, Chromatin, Chromatography, Affinity, DNA-Binding Proteins, HeLa Cells, Histones, Humans, Kidney, Male, Methylation, Organ Specificity, Peptide Fragments, Protein Processing, Post-Translational, Testis, Proteome, Protein Interaction Mapping, Proteomics, Mice, Tandem Mass Spectrometry
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