%0 Journal Article
%T Quantitative analysis of histone exchange for transcriptionally active chromatin
%A Stephanie D Byrum
%A Sean D Taverna
%A Alan J Tackett
%J Journal of Clinical Bioinformatics
%D 2011
%I BioMed Central
%R 10.1186/2043-9113-1-17
%X We previously used an isotopic labeling technique combining affinity purification and mass spectrometry called transient isotopic differentiation of interactions as random or targeted (transient I-DIRT) to identify the amounts of chemical cross-linking required to prevent histone exchange during chromatin purification. New bioinformatic analyses reported here reveal that histones containing transcription activating PTMs exchange more rapidly relative to bulk histones and therefore require a higher level of cross-linking to preserve the in vivo chromatin structure.The bioinformatic approach described here is widely applicable to other studies requiring the analysis and purification of cognate histones and their modifications. Histones containing PTMs correlated to active gene transcription exchange more readily than bulk histones; therefore, it is necessary to use more rigorous in vivo chemical cross-linking to stabilize these marks during chromatin purification.Eukaryotic genomes are highly organized into transcriptionally active (euchromatic) and silent (heterochromatic) chromatin regions. Conversion of chromatin between the two major forms is regulated in part through interactions between chromatin-modifying enzymes and nucleosomes. Nucleosomes are the fundamental unit of chromatin and consist of approximately 147 base pairs of DNA wrapped around an octameric core of the histones H2A, H2B, H3, and H4 [1]. Chromatin structure plays a key role in the regulation of gene activity and its mis-regulation is a theme characteristic of many types of disease and cancer [1]. The N-terminal tails of histones, which protrude outside of the nucleosome core [2], are subject to many sites and types of post-translational modifications (PTMs), which, in turn, help regulate biological processes through altering nucleosome stability or the function of chromatin-associated complexes [3,4]. For example, acetylation of histone lysine residues on the N-terminal tail has been correlated t
%K cross-linking
%K histone
%K post-translational modification
%K chromatin
%K affinity purification
%U http://www.jclinbioinformatics.com/content/1/1/17