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ScMNase-seq measures chromatin accessibility and nucleosome positioning in single cells

ABSTRACT: Nucleosome positioning is critical to chromatin accessibility, and is associated with gene expression programs in cells. Previous nucleosome mapping methods assemble profiles from cell populations and reveal a cell-averaged pattern: nucleosomes are positioned and form a phased array surrounding the transcription start sites (TSSs ) of active genes and DNase I hypersensitive sites (DHSs). However, cells exhibit remarkable expression heterogeneity in response to active signaling even in a homogenous population of cells, which may be related to the heterogeneity in chromatin accessibility. Here, we report a technique, termed single-cell MNase-seq (scMNase-seq), to measure genome-wide nucleosome positioning and chromatin accessibility simultaneously in single cells. Application of scMNase-seq to NIH3T3, mouse primary naïve CD4 T and embryonic stem cells (mESC) reveals two novel principles of nucleosome organization: (1) nucleosomes surrounding TSSs of silent genes or in heterochromatin regions show large positioning variation across different cells but are highly uniformly spaced along the nucleosome array and, (2) In contrast, nucleosomes surrounding TSSs of active genes and DHSs show small positioning variation across different cells but show relatively low spacing uniformness along the nucleosome array. We found a bimodal distribution of nucleosome spacing at DHSs, which corresponds to inaccessible and accessible states and is associated with nucleosome variation and accessibility variation across cells. Nucleosome variation within single cells is smaller than that across cells and variation within the same cell type is smaller than that across cell types. A large fraction of naïve CD4 T cells and mESCs show depleted nucleosome occupancy at the de novo enhancers detected in their respectively differentiated lineages, revealing the existence of cells primed for differentiation to specific lineages in undifferentiated cell populations.

ORGANISM(S): Mus musculus

PROVIDER: GSE96688 | GEO | 2018/07/23

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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ScMNase-seq measures chromatin accessibility and nucleosome positioning in single cells

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