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Dynamic changes in chromatin accessibility and nucleosome positioning in the control of antigen receptor rearrangement

ABSTRACT: Dynamic changes in chromatin accessibility and nucleosome positioning in the control of antigen receptor rearrangement

PROVIDER: PRJNA546258 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9200770_1.fastq.gz	Fastqsanger.gz
	SRR9200770_2.fastq.gz	Fastqsanger.gz
	SRR9200780_1.fastq.gz	Fastqsanger.gz
	SRR9200780_2.fastq.gz	Fastqsanger.gz
	SRR9200790_1.fastq.gz	Fastqsanger.gz

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Dynamic changes in chromatin accessibility and nucleosome positioning in the control of antigen receptor rearrangement

Project description:Developing lymphocytes diversify their antigen receptor (AgR) loci by V(D)J recombination. Here, we use a low-input version of the MACC (MNase Accessibility) assay to define the chromatin accessibility landscape of primary cells during lymphoid development tracking the changes as different AgR loci become primed for recombination. Distinct chromatin structures define unique features of IgH, Igk and TCRα loci. In particular, we find locus-specific temporal changes in accessibility both across megabase-long AgR loci and locally at the recombination signal sequences (RSSs). These changes appear to be regulated independently. We further identify local dynamic rearrangements of individual nucleosomes at RSSs during B-cell commitment. As predicted by the original “accessibility” hypothesis, these changes correlate with AgR lymphoid lineage and developmental-stage specificity. We suggest that local and global changes in chromatin openness, in concert with nucleosome occupancy and histone modifications, represent additional regulatory layers for governing the temporal order of AgR recombination.

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Dynamic regulation of nucleosome positioning in the human genome

Project description:The positioning of nucleosomes with respect to DNA plays an important role in regulating transcription. However, nucleosome mapping has been performed for only limited genomic regions in humans. We have generated genome-wide maps of nucleosome positions in both resting and activated human CD4+ T cells by direct sequencing of nucleosome ends using the Solexa high-throughput sequencing technique. We find that nucleosome phasing relative to the transcription start sites (TSSs) is directly correlated to RNA polymerase II binding. Furthermore, the first nucleosome downstream of TSSs exhibits differential positioning in active and silent genes. TCR signaling induces extensive nucleosome reorganization in promoters and enhancers to allow transcriptional activation or repression. Our results suggest that H2A.Z-containing and modified nucleosomes are preferentially lost from the -1 nucleosome position. Our data provide a comprehensive view of the nucleosome landscape and its dynamic regulation in the human genome. This microarray dataset is the gene expression data from resting and activated CD4+ T cells. We used this data to look at nucleosome positioning, Pol II and a few chromatin modifications at genes that are silent and activated in both resting and activated T cells as well as genes that are induced or repressed with T cell activation. Keywords: nucleosome mapping, expression data complementary to Solexa ChIP-Seq data

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Ki67-mediated chromatin accessibility impedes B-cell antigen-receptor gene rearrangement

Project description:B and T cells can recognise and respond to a vast array of foreign pathogens by virtue of the diverse antigen-receptor repertoire generated by gene rearrangement during development. Here, we show that deficiency in Ki67, a nuclear protein ubiquitously expressed throughout the cell cycle, impairs B-cell development at specific, early stages. We identified that Ki67 maintains global chromatin accessibility in lymphocyte progenitors at stages where antigen-receptor gene rearrangements occur and that gene rearrangement is less efficient in the absence of Ki67. That the defects in B cell development are caused by disrupted antigen-receptor gene rearrangement is shown by pre-rearranged antigen-receptor genes fully compensating for loss of Ki67. Collectively, these results identify a unique contribution from Ki67 to somatic antigen-receptor gene rearrangement.

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Project description: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.

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Nucleosome positioning for 4 yeast species

Project description:We describe the genome-wide nucleosome profiles of four related yeast species. All species display the same global organization features first described in S. cerevisiae: a stereotypical nucleosome organization along genes, and the classification of promoters into these which contain or lack a pronounced Nucleosome Depleted region (NDR), with the latter displaying a more dynamic pattern of gene expression. This global similarity, however, does not reflect a static evolutionary pattern, as nucleosome positioning at specific genes diverged rapidly leaving practically no similarity between S. cerevisiae and C. glabrata orthologs (~50 Myr). We show that this rapid divergence in nucleosome positioning contrasts a conserved pattern of gene expression, consistent with the idea that divergence of nucleosome patterns has a limited effect on gene expression as many different configurations can support the same regulatory outcome.

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