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Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE89684 | GEO | 2017/03/29

SECONDARY ACCESSION(S): PRJNA352947

REPOSITORIES: GEO

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Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells.

Project description:Epigenetic mechanisms, including chromatin structure, chromatin dynamics and histone modifications play an important role for maintenance and differentiation of pluripotent embryonic stem cells. However, little is known about the molecular mechanisms of adult stem cell specification and differentiation. Here, we used intestinal stem cells (ISCs) as a model system to reveal the epigenetic changes coordinating gene expression programs during these processes. We found that two distinct epigenetic mechanisms participate in establishing the transcriptional program promoting ISC specification from embryonic progenitors. A large number of adult ISC signature genes are targets of repressive DNA methylation in embryonic intestinal epithelial progenitors. On the other hand, genes essential for embryonic development acquire H3K27me3 and are silenced during ISC specification. We also show that the repression of ISC signature genes as well as the activation of enterocyte specific genes is accompanied by a global loss of H2A.Z during ISCs differentiation. Our results reveal that, already during ISC specification, an extensive remodeling of chromatin both at promoters and distal regulatory elements organizes transcriptional landscapes operating in differentiated enterocytes, thus explaining similar chromatin modification patterns in the adult gut epithelium.

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Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells [rnaseq]

Project description:To follow the changes in the transcriptional programs accompanying the specification, maintenance and differentiation of the adult ISCs we sequenced whole transcriptomes of embryonic intestinal epithelium progenitors (at E12.5 and E14.5), adult ISCs and their differentiated progenies, the majority of which are absorptive enterocytes. EpCAM positive embryonic gut epithelium was isolated from dissected small intestines using fluorescence activated cell sorting (FACS). Adult ISCs were purified on the basis of GFP fluorescence from crypts of Lgr5GFP-Cre-ERT mice (Barker et al. 2007), whereas enterocytes (EpCAM+ CD45- CD31-) were isolated from villi.

2017-03-29 | GSE89683 | GEO

Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells [mbd]

Project description:We assessed whether changes in DNA methylation were associated with the regulation of ISC signature genes. Methylated regions of DNA from whole genome were isolated using Methyl Binding Domain pull-down followed by sequencing (MBD-seq). The size of DNA fragments was between 120 to 170 bp, which provides a resolution at nucleosome level.

2017-03-29 | GSE89682 | GEO

Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells [k27m3]

Project description:To determine chromatin changes associated with ISCs specification we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using 2x105 FACS purified E12.5 or E14.5 embryonic intestinal epithelial cells, Lgr5+ adult ISCs and enterocytes.

2017-03-29 | GSE89681 | GEO

Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells [k27ac]

2017-03-29 | GSE89680 | GEO

Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells [k4m3]

Project description:To determine chromatin changes associated with ISCs specification we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using 2x10e5 FACS purified E12.5 or E14.5 embryonic intestinal epithelial cells, Lgr5+ adult ISCs and enterocytes.

2017-03-29 | GSE89679 | GEO

Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells [h2az]

Project description:To determine chromatin changes associated with ISCs specification we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using 2x10e5 FACS purified E12.5 or E14.5 embryonic intestinal epithelial cells, Lgr5+ adult ISCs and enterocytes.

2017-03-29 | GSE89678 | GEO

Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells

Project description:Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells

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Dynamic landscape of chromatin accessibility and transcriptomic changes during differentiation of human embryonic stem cells into dopaminergic neurons.

Project description:Chromatin architecture influences transcription by modulating the physical access of regulatory factors to DNA, playing fundamental roles in cell identity. Studies on dopaminergic differentiation have identified coding genes, but the relationship with non-coding genes or chromatin accessibility remains elusive. Using RNA-Seq and ATAC-Seq we profiled differentially expressed transcripts and open chromatin regions during early dopaminergic neuron differentiation. Hierarchical clustering of differentially expressed genes, resulted in 6 groups with unique characteristics. Surprisingly, the abundance of long non-coding RNAs (lncRNAs) was high in the most downregulated transcripts, and depicted positive correlations with target mRNAs. We observed that open chromatin regions decrease upon differentiation. Enrichment analyses of accessibility depict an association between open chromatin regions and specific functional pathways and gene-sets. A bioinformatic search for motifs allowed us to identify transcription factors and structural nuclear proteins that potentially regulate dopaminergic differentiation. Interestingly, we also found changes in protein and mRNA abundance of the CCCTC-binding factor, CTCF, which participates in genome organization and gene expression. Furthermore, assays demonstrated co-localization of CTCF with Polycomb-repressed chromatin marked by H3K27me3 in pluripotent cells, progressively decreasing in neural precursor cells and differentiated neurons. Our work provides a unique resource of transcription factors and regulatory elements, potentially involved in the acquisition of human dopaminergic neuron cell identity.

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Project description:Multipotent mesenchymal stromal cells (MSCs) are critical for regeneration of multiple tissues. Epigenetic mechanisms are fundamental regulators of lineage specification and cell fate, and as such, we addressed the question of which epigenetic modifications characterize the transition of nascent MSCs to a tissue specific MSC-derived phenotype. By profiling the temporal changes of seven histone marks correlated to gene expression during proliferation, early commitment, matrix deposition, and mineralization stages, we identified distinct epigenetic mechanisms that regulate transcriptional programs necessary for tissue-specific phenotype development. Patterns of stage-specific enrichment of histone modifications revealed distinct modes of repression and activation of gene expression that would not be detected using single endpoint analysis. We discovered that at commitment, H3K27me3 is removed from genes that are upregulated and is not acquired on downregulated genes. Additionally, we found that the absence of H3K4me3 modification at promoters defined a subset of osteoblast-specific upregulated genes, indicating that acquisition of acetyl modifications drive activation of these genes. Significantly, loss or gain of H3K36me3 was the primary predictor of dynamic changes in temporal gene expression. Using unsupervised pattern discovery analysis the signature of osteogenic-related histone modifications identified novel functional cis regulatory modules associated with enhancer regions that control tissue-specific genes. Our work provides a cornerstone to understand the epigenetic regulation of transcriptional programs that are important for MSC lineage commitment and lineage, as well as insights to facilitate MSC-based therapeutic interventions.

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