ArticleEpigenetics & chromatin2017
Metabolic labeling in middle-down proteomics allows for investigation of the dynamics of the histone code.
Article in Epigenetics & chromatin, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed, 45 citations in OpenAlex.
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- Mass Spectrometry Quantification of Epigenetic Changes: A Scoping Review for Cancer and Beyond.International journal of molecular sciences · 2025Article
- Loss of CARM1 alters the developmental programming of Glioma stem-like cells and creates a druggable NGFR/NTRK dependency.bioRxiv : the preprint server for biology · 2025Article
- Automated Sample Preparation for the Unbiased Analysis of Histone Posttranslational Modifications Via Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Optimized and Robust Workflow for Quantifying the Canonical Histone Ubiquitination Marks H2AK119ub and H2BK120ub by LC-MS/MS.Journal of proteome research · 2024Article
- Enrichment of histone tail methylated lysine residuesChemical science · 2024Article
- Cancer-associated Histone H3 N-terminal arginine mutations disrupt PRC2 activity and impair differentiation.Nature communications · 2024Article
- An optimized and robust workflow for quantifying the canonical histone ubiquitination marks H2AK119ub and H2BK120ub by LC-MS/MS.bioRxiv : the preprint server for biology · 2024Article
- Decoding Ubiquitin Modifications by Mass Spectrometry.Advances in experimental medicine and biology · 2024Review
- Streamlined quantitative analysis of histone modification abundance at nucleosome-scale resolution with siQ-ChIP version 2.0.Scientific reports · 2023Article
- The Next Frontier: Translational Development of Ubiquitination, SUMOylation, and NEDDylation in Cancer.International journal of molecular sciences · 2022Review
- Precision Medicine: An Optimal Approach to Patient Care in Renal Cell Carcinoma.Frontiers in medicine · 2022Review
- Understanding the Phytoremediation Mechanisms of Potentially Toxic Elements: A Proteomic Overview of Recent Advances.Frontiers in plant science · 2022Review
- Combinatorial Histone H3 Modifications Are Dynamically Altered in Distinct Cell Cycle Phases.Journal of the American Society for Mass Spectrometry · 2021Article
- Mapping Influenza-Induced Posttranslational Modifications on Histones from CD8+ T Cells.Viruses · 2020Article
- Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis.Methods (San Diego, Calif.) · 2020Article
- Proposed Neuroimmune Roles of Dimethyl Fumarate, Bupropion,Brain sciences · 2020Review
- Mass Spectrometry to Study Chromatin Compaction.Biology · 2020Review
- Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy.Nature genetics · 2020Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
backgroundMiddle-down mass spectrometry (MS), i.e., analysis of long (~50-60 aa) polypeptides, has become the method with the highest throughput and accuracy for the characterization of combinatorial histone posttranslational modifications (PTMs). The discovery of histone readers with multiple domains, and overall the cross talk of PTMs that decorate histone proteins, has revealed that histone marks have synergistic roles in modulating enzyme recruitment and subsequent chromatin activities. Here, we demonstrate that the middle-down MS strategy can be combined with metabolic labeling for enhanced quantification of histone proteins and their combinatorial PTMs in a dynamic manner.
methodsWe used a nanoHPLC-MS/MS system consisting of hybrid weak cation exchange-hydrophilic interaction chromatography combined with high resolution MS and MS/MS with ETD fragmentation. After spectra identification, we filtered confident hits and quantified polypeptides using our in-house software isoScale.
resultsWe first verified that middle-down MS can discriminate and differentially quantify unlabeled from heavy labeled histone N-terminal tails (heavy lysine and arginine residues). Results revealed no bias toward identifying and quantifying unlabeled versus heavy labeled tails, even if the heavy labeled peptides presented the typical skewed isotopic pattern typical of long protein sequences that hardly get 100% labeling. Next, we plated epithelial cells into a media with heavy methionine-(methyl-
conclusionsWe demonstrate that middle-down MS, despite being a more scarcely exploited MS technique than bottom-up, is a robust quantitative method for histone PTM characterization. In particular, middle-down MS combined with metabolic labeling is currently the only methodology available for investigating turnover of combinatorial histone PTMs in dynamic systems.
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