proteogenomic characterization and mapping of nucleosomes decoded by brd and hp1 proteinsproteogenomic表征和映射的核小体解码brd和hp1蛋白.pdfVIP

LeRoy et al. Genome Biology 2012, 13:R68 /2012/13/8/R68 RESEARCH Open Access Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins 1† 2† 1 1 1,3 2 Gary LeRoy , Iouri Chepelev , Peter A DiMaggio , Mario A Blanco , Barry M Zee , Keji Zhao and Benjamin A Garcia1,3,4,5* Abstract Background: Histone post-translational modifications (PTMs) constitute a branch of epigenetic mechanisms that can control the expression of eukaryotic genes in a heritable manner. Recent studies have identified several PTM- binding proteins containing diverse specialized domains whose recognition of specific PTM sites leads to gene activation or repression. Here, we present a high-throughput proteogenomic platform designed to characterize the nucleosomal make-up of chromatin enriched with a set of histone PTM binding proteins known as histone PTM readers. We support our findings with gene expression data correlating to PTM distribution. Results: We isolated human mononucleosomes bound by the bromodomain-containing proteins Brd2, Brd3 and Brd4, and by the chromodomain-containing heterochromatin proteins HP1b and HP1a. Histone PTMs were quantified by mass spectrometry (ChIP-qMS), and their associated DNAs were mapped using deep sequencing. Our results reveal that Brd- and HP1-bound nucleosomes are enriched in histone PTMs consistent with actively transcribed euchromatin and silent heterochromatin, respectively. Data collected using RNA-Seq show that Brd- bound sites correlate with highly expressed genes. In particular, Brd3 and Brd4 are most enriched on nucleosomes located within HOX gene clusters, whose expression is reduced upon Brd4 depletion by short hairpin RNA. Conclusion