Dataset Information

Genome-wide measurement of chromatin accessibility by RED-seq

ABSTRACT: Differential accessibility of DNA to nuclear proteins underlies the regulation of numerous cellular processes. DNA accessibility is primarily determined by the presence or absence of nucleosomes. At present, methods for mapping the positions and occupancy of nucleosomes genome-wide (MNase-seq) have uncovered the nucleosomal landscapes of different cell types and organisms. Conversely, methods specialized for the detection of large nucleosome-free regions of chromatin (DNase-seq, FAIRE-seq) have uncovered numerous gene regulatory elements. However, these methods are less successful in measuring the accessibility of DNA sequences within nucelosome arrays. Here we describe a new genome-wide method, RED-seq (deep sequencing analysis of Restriction Enzyme Digestion), that measures chromatin accessibility in an unbiased way. Using this method, we identified differences in chromatin accessibility between populations of cells, not only in broadly nucleosome-depleted regions of the genome (e.g., enhancers and promoters), but also within the more widespread regions of nucleosomal occupancy. Furthermore, RED-seq identified both large differences in chromatin accessibility in distinct cell lineages and subtle changes observed during differentiation of mouse embryonic stem cells (ESCs). Most notably, using RED-seq, we detected differences in accessibility among sequences occupied by distinct nucleosome variants. Therefore, RED-seq provides unique insights into genome-wide chromatin dynamics.

ORGANISM(S): Mus musculus

PROVIDER: GSE51821 | GEO | 2014/12/31

SECONDARY ACCESSION(S): PRJNA225488

REPOSITORIES: GEO

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Project description:Nucleosome positioning dictates the DNA accessibility for regulatory proteins, and thus is critical for gene expression and regulation. It has been well documented that only a subset of nucleosomes are reproducibly positioned (phased) in eukaryotic genomes. The most prominent example of phased nucleosomes is the context of genes, where phased nucleosomes flank the transcriptional starts sites (TSSs). It is unclear, however, what factors influence nucleosome phasing in regions that are not close to genes. We performed a combinational mapping of nucleosome positioning and DNase I hypersensitive sites (DHSs) across the rice genome. We discovered that DHSs located in a variety of contexts, both genic and intergenic, were flanked by strongly phased nucleosome arrays. Our results support the barrier model for nucleosome organization as a general feature of eukaryote genomes, including plant genomes, and not limited to TSSs. Specifically, regions bound with regulatory proteins, including intergenic regions, can serve as barriers that organize phased nucleosome arrays on both sides. Our results also suggest that rice DHSs often span a single, phased nucleosome, similar to the H2A.Z-containing nucleosomes observed in DHSs in the human genome. We propose that genome-wide nucleosome positioning in the eukaryotic genomes is orchestrated by genomic regions associated with regulatory proteins. Rice chromatin was digested by micrococcal nuclease (MNase) into mono-nucleosome size. Mono-nucleosomal DNA was isolated and sequenced (MNase-seq) using Illumina sequencing platforms. We obtained a total of 38 million (M) single-end reads from our first MNase-seq experiment and mapped ~26 M to unique positions in the rice genome. We also conducted pair-end sequencing of an independent MNase-seq library, obtained 274 M paired-end reads, and mapped ~231 M read pairs to unique positions in the rice genome.We applied a strategy of combinational mapping of nucleosome positioning and DHSs (GSE26610) to examine whether nucleosome positioning is associated with all cis-regulatory elements in the rice genome. All datasets used in the analysis were developed using rice leaf tissue in the same developmental stage

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Genome-wide measurement of chromatin accessibility by RED-seq

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