Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response

Abstract

Nucleosome occupancy is critically important in regulating access to the eukaryotic genome. Few studies in human cells have measured genome-wide nucleosome distributions at high temporal resolution during a response to a common stimulus. We measured nucleosome distributions at high temporal resolution following Kaposi's-sarcoma-associated herpesvirus (KSHV) reactivation using our newly developed mTSS-seq technology, which maps nucleosome distribution at the transcription start sites (TSS) of all human genes. Nucleosomes underwent widespread changes in organization 24 hours after KSHV reactivation and returned to their basal nucleosomal architecture 48 hours after KSHV reactivation. The widespread changes consisted of an indiscriminate remodeling event resulting in the loss of nucleosome rotational phasing signals. Additionally, one in six TSSs in the human genome possessed nucleosomes that are translationally remodeled. 72% of the loci with translationally remodeled nucleosomes have nucleosomes that moved to positions encoded by the underlying DNA sequence. Finally we demonstrated that these widespread alterations in nucleosomal architecture potentiated regulatory factor binding. These descriptions of nucleosomal architecture changes provide a new framework for understanding the role of chromatin in the genomic response, and have allowed us to propose a hierarchical model for chromatin-based regulation of genome response.

Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J recombination

“…Assuming that adjacent nucleosomes (on the intergenic side of the RSS) are separated by distances similar to those detected for phased nucleosomes at transcription start sites (36,37), enough room is left for the 39 bp of the RSS (where the RSS is placed at coordinates 0 to +38) to be located off the histone core shoulder. Thus, in pro-B cells, the RSS would be either loosely associated with the nucleosome or in the linker region adjacent to the nucleosome, an ideal location that would allow access to the RAG recombinase (20,23).…”

“…Variability in MNase profiles between experiments carried out under different conditions can hinder a direct comparison of absolute levels of nucleosome occupancy between cell types (35). However, the patterns across a locus can be readily compared between cell types, and a comparison of nucleosome occupancy across a locus within an individual cell type can be made (36)(37)(38)(39). Thus, our study focused on a comparison of relative values of nucleosome occupancy.…”

“…MNase cleavage and purification were performed as described (37,66). Briefly, chromatin from fixed nuclei was digested in MNase digestion buffer (25 mM KCl, 4 mM MgCl 2 , 1 mM CaCl 2 , 12.5% glycerol, and 50 mM Tris·HCl, pH 7.4) with titrated amounts of MNase (Worthington) for 5 min at 37°C (Fig.…”

MNase profiling of promoter chromatin inS. typhimurium-stimulated GM12878 cells reveals dynamic and response-specific nucleosome architecture

“…Previously, we combined MNase-seq with in-solution targeted enrichment of 2 kb surrounding TSSs of 21,857 human genes (Druliner et al, 2016; Sexton et al, 2016), as curated by NCBI RefSeq (Pruitt et al, 2009). We termed this approach Transcription Start Site MNase-seq (mTSS-seq).…”

“…Micrococcal nuclease (MNase) was first used to isolate nucleosomal DNA from the chicken beta-globin gene (Sun et al, 1986). It remains the predominant method for generation of nucleosome occupancy maps in eukaryotic genomes, and previous studies have mapped changes in chromatin structure during differentiation, environmental stimulus or stress, and disease states (Shivaswamy et al, 2008; Teif et al, 2012; Druliner et al, 2013; Sexton et al, 2014, Sexton et al, 2016). Additionally, it has been recently shown that nucleosomes exhibit differential sensitivity to MNase.…”