Recognition of a Mononucleosomal Histone Modification Pattern by BPTF via Multivalent Interactions

Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
Cell (Impact Factor: 32.24). 05/2011; 145(5):692-706. DOI: 10.1016/j.cell.2011.03.053
Source: PubMed


Little is known about how combinations of histone marks are interpreted at the level of nucleosomes. The second PHD finger of human BPTF is known to specifically recognize histone H3 when methylated on lysine 4 (H3K4me2/3). Here, we examine how additional heterotypic modifications influence BPTF binding. Using peptide surrogates, three acetyllysine ligands are indentified for a PHD-adjacent bromodomain in BPTF via systematic screening and biophysical characterization. Although the bromodomain displays limited discrimination among the three possible acetyllysines at the peptide level, marked selectivity is observed for only one of these sites, H4K16ac, in combination with H3K4me3 at the mononucleosome level. In support, these two histone marks constitute a unique trans-histone modification pattern that unambiguously resides within a single nucleosomal unit in human cells, and this module colocalizes with these marks in the genome. Together, our data call attention to nucleosomal patterning of covalent marks in dictating critical chromatin associations.

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Available from: Haitao Li, Feb 23, 2015
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    • "The analysis will need to be modified to include the interactions between histones PTMs and their matching readers and associated proteins (Musselman et al. 2012). The complexity of the analysis of mechanisms directing interactions between readers and histone PTMs increased when researchers realized that neighboring PTMs influence the readers' recognition (Macdonald et al. 2005; Ruthenburg et al. 2011; for review, see Musselman et al. 2012). The same core histone harboring bivalent PTMs, within a single nucleosome, may be recognized by multiple readers, leading to different biological outcomes. "
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    • "Recently the NCL strategy was further developed to construct a disulfide-linked uH2B for structural analysis of hDot1L's activity and its stimulation mechanism [91]. Ruthenburg and co-workers incubated the EPL-synthesized radioactively labeled nucleosome with immobilized BPTF PHD-Bromo domain to confirm the interaction of BPTF PHD-Bromo domain with both H3K4me3 and H4K16ac [70]. To investigate the interaction between DNA methylation and HPTMs, Bartke and co-workers developed a novel analytical technique so-called SILAC Nucleosome Affinity Purification (SNAP) strategy based on EPL method [22]. "
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    • "ITC experiments were carried out at UNC Macromolecular Interactions Facility using a MicroCal AutoITC-200 system (GE Healthcare). Typically, peptides and proteins were subject to extensive dialysis against the same buffer, and ITC titrations were performed at 4-6°C in a buffer consisting of 100 mM NaCl, 20 mM Tris-HCl pH 7.5, and 2mM beta-mercaptoethanol using a previously described protocol (Ruthenburg et al., 2011; Wang et al., 2009). Proteins at concentrations of ~ 70-200 µM were loaded into the ITC cell and peptides at 10-15 fold higher concentrations were loaded into the ITC syringe. "

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