ArticleNucleic acids research2015
Identification of protein complexes that bind to histone H3 combinatorial modifications using super-SILAC and weighted correlation network analysis.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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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
19 citing papers in PubMed, 40 citations in OpenAlex.
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- Chemical Biology Approaches to Identify and Profile Interactors of Chromatin Modifications.ACS chemical biology · 2023Review
- Motoneurons innervation determines the distinct gene expressions in multinucleated myofibers.Cell & bioscience · 2022Article
- Metabolomics Analysis Coupled with Weighted Gene Co-Expression Network Analysis Unravels the Associations of Tricarboxylic Acid Cycle-Intermediates with Edible Pigments Produced byFoods (Basel, Switzerland) · 2022Article
- Contrast-Enhanced Computed Tomography-Based Radiogenomics Analysis for Predicting Prognosis in Gastric Cancer.Frontiers in oncology · 2022Article
- Repression of germline genes by PRC1.6 and SETDB1 in the early embryo precedes DNA methylation-mediated silencing.Nature communications · 2021Article
- Human Histone Interaction Networks: An Old Concept, New Trends.Journal of molecular biology · 2021Article
- Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method.Scientific reports · 2020Article
- Identification of biomarkers associated with histological grade and prognosis of gastric cancer by co-expression network analysis.Oncology letters · 2019Article
- The gene repressor complex NuRD interacts with the histone variant H3.3 at promoters of active genes.Genome research · 2018Article
- Identification of Biomarkers Associated With Pathological Stage and Prognosis of Clear Cell Renal Cell Carcinoma by Co-expression Network Analysis.Frontiers in physiology · 2018Article
- Identifying biomarkers of papillary renal cell carcinoma associated with pathological stage by weighted gene co-expression network analysis.Oncotarget · 2017Article
- Co-expression network analysis identified FCER1G in association with progression and prognosis in human clear cell renal cell carcinoma.International journal of biological sciences · 2017Article
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- Regulation of Methyllysine Readers through Phosphorylation.ACS chemical biology · 2016Article
- Studying epigenetic complexes and their inhibitors with the proteomics toolbox.Clinical epigenetics · 2016Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
The large number of chemical modifications that are found on the histone proteins of eukaryotic cells form multiple complex combinations, which can act as recognition signals for reader proteins. We have used peptide capture in conjunction with super-SILAC quantification to carry out an unbiased high-throughput analysis of the composition of protein complexes that bind to histone H3K9/S10 and H3K27/S28 methyl-phospho modifications. The accurate quantification allowed us to perform Weighted correlation network analysis (WGCNA) to obtain a systems-level view of the histone H3 histone tail interactome. The analysis reveals the underlying modularity of the histone reader network with members of nuclear complexes exhibiting very similar binding signatures, which suggests that many proteins bind to histones as part of pre-organized complexes. Our results identify a novel complex that binds to the double H3K9me3/S10ph modification, which includes Atrx, Daxx and members of the FACT complex. The super-SILAC approach allows comparison of binding to multiple peptides with different combinations of modifications and the resolution of the WGCNA analysis is enhanced by maximizing the number of combinations that are compared. This makes it a useful approach for assessing the effects of changes in histone modification combinations on the composition and function of bound complexes.
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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.