ABSTRACT
Recently discovered histone lysine acylation marks increase the functional diversity of nucleosomes well beyond acetylation. Here, we focus on histone butyrylation in the context of sperm cell differentiation. Specifically, we investigate the butyrylation of histone H4 lysine 5 and 8 at gene promoters where acetylation guides the binding of Brdt, a bromodomain-containing protein, thereby mediating stage-specific gene expression programs and post-meiotic chromatin reorganization. Genome-wide mapping data show that highly active Brdt-bound gene promoters systematically harbor competing histone acetylation and butyrylation marks at H4 K5 and H4 K8. Despite acting as a direct stimulator of transcription, histone butyrylation competes with acetylation, especially at H4 K5, to prevent Brdt binding. Additionally, H4 K5K8 butyrylation also marks retarded histone removal during late spermatogenesis. Hence, alternating H4 acetylation and butyrylation, while sustaining direct gene activation and dynamic bromodomain binding, could impact the final male epigenome features.
Subject(s)
Butyrates/metabolism , Epigenesis, Genetic , Gene Expression Regulation, Developmental , Histones/metabolism , Nuclear Proteins/genetics , Promoter Regions, Genetic , Protein Processing, Post-Translational , Spermatocytes/metabolism , Acetylation , Animals , Binding Sites , Cell Differentiation , Chromatin Assembly and Disassembly , Genome-Wide Association Study , Histones/chemistry , Histones/genetics , Lysine , Male , Mice , Nuclear Proteins/chemistry , Nuclear Proteins/metabolism , Protein Conformation , Structure-Activity Relationship , Transcription, Genetic , Transcriptional ActivationABSTRACT
Methylation of lysine residues on histone proteins is known to play an important role in chromatin structure and function. However, non-histone protein substrates of this modification remain largely unknown. An effective approach for system-wide analysis of protein lysine methylation, particularly lysine monomethylation, is lacking. Here we describe a chemical proteomics approach for global screening for monomethyllysine substrates, involving chemical propionylation of monomethylated lysine, affinity enrichment of the modified monomethylated peptides, and HPLC/MS/MS analysis. Using this approach, we identified with high confidence 446 lysine monomethylation sites in 398 proteins, including three previously unknown histone monomethylation marks, representing the largest data set of protein lysine monomethylation described to date. Our data not only confirms previously discovered lysine methylation substrates in the nucleus and spliceosome, but also reveals new substrates associated with diverse biological processes. This method hence offers a powerful approach for dynamic study of protein lysine monomethylation under diverse cellular conditions and in human diseases.
Subject(s)
Lysine/metabolism , Proteomics/methods , Amino Acid Sequence , Antibodies/metabolism , Cell Line , Computational Biology , Humans , Isotope Labeling , Methylation , Molecular Sequence Data , Peptides/chemistry , Peptides/metabolism , Proteome/metabolism , Reproducibility of ResultsABSTRACT
BACKGROUND: Borna disease virus (BDV) replicates in the nucleus and establishes persistent infections in mammalian hosts. A human BDV strain was used to address the first time, how BDV infection impacts the proteome and histone lysine acetylation (Kac) of human oligodendroglial (OL) cells, thus allowing a better understanding of infection-driven pathophysiology in vitro. METHODS: Proteome and histone lysine acetylation were profiled through stable isotope labeling for cell culture (SILAC)-based quantitative proteomics. The quantifiable proteome was annotated using bioinformatics. Histone acetylation changes were validated by biochemistry assays. RESULTS: Post BDV infection, 4383 quantifiable differential proteins were identified and functionally annotated to metabolism pathways, immune response, DNA replication, DNA repair, and transcriptional regulation. Sixteen of the thirty identified Kac sites in core histones presented altered acetylation levels post infection. CONCLUSIONS: BDV infection using a human strain impacted the whole proteome and histone lysine acetylation in OL cells.
Subject(s)
Borna Disease/metabolism , Borna disease virus/physiology , Histones/metabolism , Oligodendroglia/metabolism , Proteome/metabolism , Acetylation , Amino Acid Motifs , Amino Acid Sequence , Borna Disease/genetics , Borna Disease/virology , Female , Histones/chemistry , Histones/genetics , Humans , Lysine/metabolism , Molecular Sequence Data , Oligodendroglia/virology , Proteome/genetics , ProteomicsABSTRACT
Suberoylanilide hydroxamic acid (SAHA) is a well-known pan HDAC inhibitor, and its clinical application (Vorinostat) has been demonstrated to treat nonsmall cell lung cancer (NSCLS). Nevertheless, the impact of SAHA treatment on histone lysine acetylation and proteome in NSCLS cells still need further elucidate. In NSCLS A549 cells, by using stable isotope labeling for cell culture (SILAC)-based quantitative proteomics, biochemistry assay, and bioinformatic analysis, here we for the first time comprehensively identified and quantified histone lysine acetylation in A549 cells toward SAHA treatment. Despite the fact that SAHA treatment significantly increased histone lysine acetylation in specific sites, unexpectedly, some important "histone markers" showed markedly decreased acetylation level. Further quantitative proteome studies showed that among totally quantifiable 2818 nonredundant proteins, 1355 proteins were with increased level and 1463 with decreased level in response to SAHA treatment. Bioinformatic analysis further revealed that those quantifiable proteins were mainly involved in multiple biological functions and metabolic and enzyme-regulated pathways as well as protein complexes. By establishing the link between histone modification and whole proteome in response to SAHA treatment in NSCLS cells, this study therefore may deepen our understanding of HDAC inhibitor-mediated cancer therapeutics.
