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Genome-wide maps of chromatin state in HSC, Pro B and mature B cells

ABSTRACT: We have used a genome-wide ChIP-sequencing approach to define and investigate the dynamics of the cis-regulatory landscape in three developmental stages of the murine hematopoietic system. To this end, we have compared the profiles of H3K4me3, H3K4me1, H3K27ac, H3K27me3 and H3K9me2 in HSCs, committed pro-B and splenic mature B cells. We find the enhancer repertoire to be dynamically reshaped during hematopoiesis progression, surprisingly only a small fraction of primed enhancers in HSCs or committed progenitors become activated in subsequent stages. In turn, the majority of active enhancers in terminally differentiated cells are not primed in earlier stages. We also found that The heterochromatin mark H3K9me2 covers large domains that remain largerly invariant across the three stages and are depleted in both active chromatin marks and the Polycomb related mark H3K27me3.

ORGANISM(S): Mus musculus

PROVIDER: GSE60005 | GEO | 2015/10/19

SECONDARY ACCESSION(S): PRJNA257383

REPOSITORIES: GEO

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Genome-wide maps of chromatin state in HSC, Pro B and mature B cells

Project description:We have used a genome-wide ChIP-sequencing approach to define and investigate the dynamics of the cis-regulatory landscape in three developmental stages of the murine hematopoietic system. To this end, we have compared the profiles of H3K4me3, H3K4me1, H3K27ac, H3K27me3 and H3K9me2 in HSCs, committed pro-B and splenic mature B cells. We find the enhancer repertoire to be dynamically reshaped during hematopoiesis progression, surprisingly only a small fraction of primed enhancers in HSCs or committed progenitors become activated in subsequent stages. In turn, the majority of active enhancers in terminally differentiated cells are not primed in earlier stages. We also found that The heterochromatin mark H3K9me2 covers large domains that remain largerly invariant across the three stages and are depleted in both active chromatin marks and the Polycomb related mark H3K27me3. Investigating enhancer dynamics in 3 different stages of B cell development

2015-10-19 | E-GEOD-60005 | biostudies-arrayexpress

Genome-wide maps of chromatin state in Medicago truncatula nodule and non nitrogen-starved root systems

Project description:Study of repressive marks (two heterochromatic: H3K9me2 and H3K27me1; one euchromatic: H3K27me3) and one active mark (H3K9ac) by whole-genome ChIPseq

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Regulation of mammalian 3D genome organization and histone H3K9 dimethylation by H3K9 methyltransferases

Project description:Histone H3 lysine 9 dimethylation (H3K9me2) is a highly conserved silencing epigenetic mark. Chromatin marked with H3K9me2 forms large domains in mammalian cells and overlaps well with lamina-associated domains and the B compartment defined by Hi-C. However, the role of H3K9me2 in 3-dimensional (3D) genome organization remains unclear. We investigated genome-wide H3K9me2 distribution, transcriptome, and 3D genome organization in mouse embryonic stem cells following the inhibition or depletion of five H3K9 methyltransferases (MTases): G9a, GLP, SETDB1, SUV39H1, and SUV39H2. H3K9me2 was regulated by all five MTases; however, H3K9me2 and transcription in the A and B compartments were regulated by different MTases. H3K9me2 in A compartments was primarily regulated by G9a/GLP and SETDB1, while H3K9me2 in the B compartments was regulated by all five MTases. Furthermore, decreased H3K9me2 correlated with changes to the more active compartmental state that accompanied transcriptional activation.

2021-08-05 | PXD024756 | Pride

Quantitative Dynamics of Chromatin Remodeling during Germ Cell Specification from Mouse Embryonic Stem Cells

Project description:Germ cell specification is accompanied by epigenetic remodeling, the scale and specificity of which are unclear. Here, we quantitatively delineate chromatin dynamics during induction of mouse embryonic stem cells (ESCs) to epiblast-like cells (EpiLCs) and from there into primordial germ cell-like cells (PGCLCs), revealing large-scale reorganization of chromatin signatures including H3K27me3 and H3K9me2 patterns. EpiLCs contain abundant bivalent gene promoters characterized by low H3K27me3, indicating a state primed for differentiation. PGCLCs initially lose H3K4me3 from many bivalent genes but subsequently regain this mark with concomitant upregulation of H3K27me3, particularly at developmental regulatory genes. PGCLCs progressively lose H3K9me2, including at lamina-associated perinuclear heterochromatin, resulting in changes in nuclear architecture. T recruits H3K27ac to activate BLIMP1 and early mesodermal programs during PGCLC specification, which is followed by BLIMP1-mediated repression of a broad range of targets, possibly through recruitment and spreading of H3K27me3. These findings provide a foundation for reconstructing regulatory networks of the germline epigenome.

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Genome-wide analysis of H3K9me2 and JIL-1 kinase mediated histone H3S10 phosphorylation in drosophila [ChIP-seq: 13 samples]

Project description:In this study we have determined the genome-wide relationship of JIL-1 kinase mediated H3S10 phosphorylation with gene expression and the distribution of the epigenetic H3K9me2 mark. We show in wild-type salivary gland cells that the H3S10ph mark is predominantly enriched at active genes whereas the H3K9me2 mark largely is associated with inactive genes.

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Genome-wide maps of DNA cytosine methylation state in during normal differentiation commitment in hematopoietic stem cells (HSC) and in Special AT-rich sequence-binding protein1 (Satb1) - deficient HSC

Project description:Our data show Satb1 deficiency leads to alterations in DNA cytosine methylation and a commitment-primed epigenetic state in HSCs. Examination of DNA cytosine methylation in wild type HSC and differentiation-committed progenitors as well as in wild type HSC and HSC lacking Satb1 (n=2 each).

2013-04-07 | E-GEOD-44304 | biostudies-arrayexpress

ChIP-seq analysis of hematopoetic progenitors

Project description:Bivalent chromatin refers to the simultaneous occurrence of transcription activation (H3K4me3)- and repression (H3K27me3)-associated histone modifications at gene promoters. This mark was first identified in ES cells and proposed to maintain genes in a poised state for future resolution to fully-active (H3K4me3-only) or fully-repressed (H3K27me3-only) states. In this report we rigorously test the poising hypothesis using a well-established developmental paradigm of hematopoietic stem cell differentiation to T lymphoid lineage committed cells. We show that bivalent chromatin is generated and resolved at specific stages of hematopoiesis. The epigenetic states from which it is generated and the states to which it is resolved vary with developmental stage, suggesting that bivalency serves different functions at each stage. Moreover, singly-marked genes do not transition to the opposing univalent state via a bivalent intermediate.

2018-12-31 | GSE43428 | GEO

Salt priming A. thaliana ChIP-Seq

Project description:A role of chromatin in plant memory of environmental stress has been proposed. In this study ChIP-Seq was employed to investigate whether a transient mild salt treatment of Arabidopsis thaliana plant at seedling stage (M-^Qpriming treatmentM-^R: 50 mM NaCl for 24 hours) altered genome-wide profiles of four histone modifications; H3K4me2, H3K4me3, H3K9me2 and H3K27me3. Comparison of histone modification profiles between primed and non-primed plants harvested immediately after the priming treatment showed differences in all histone modifications but were strongest and most abundant for H3K27me3. We subsequently explored whether these changes were maintained over an extensive period of growth in control conditions. Additional ChIP-Seq analysis showed that differences in the H3K27me3 profiles between primed and non-primed plants were still apparent after a growth period of ten days in control conditions. The results provide first indication for a potential role of H3K27me3 in long-term somatic memory of abiotic stress events in plants. The obtained dataset was compared with RNA-seq data measured in the same plant material (see parallel submission of RNA-Seq data in ArrayExpress: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1668).

2013-06-01 | E-MTAB-1663 | biostudies-arrayexpress

Rapid and Pervasive Changes in Genome-Wide Enhancer Usage During Mammalian Development

Project description:Here we used epigenomic profiling for H3K27ac, a mark of active enhancers to examine the genome-wide in vivo utilization of enhancers in three different mouse tissues across seven developmental stages, ranging from mid-gestation through adulthood. The majority of the ~90,000 enhancers identified exhibited tightly temporally restricted activity windows and were associated with stage-specific biological functions and regulatory pathways in individual tissues. Comparative genomic analysis revealed that evolutionary conservation of enhancers decreases following mid-gestation across all tissues examined. The dynamic enhancer activities uncovered in this study illuminate rapid and pervasive temporal in vivo changes in enhancer usage underlying developmental processes and demonstrate the value of time-course chromatin profiling of relevant tissues across development. Examination of H3K27ac in mouse forebrain, heart and liver tissues collected across developmental stages.

2013-12-19 | E-GEOD-52386 | biostudies-arrayexpress

Mapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis

Project description:Formation of the blood from self-renewing hematopoietic stem cells to terminal lineages necessarily involves epigenomic modifications of the genome to control regulator and signature gene expression. By analysing the global expression profiles of hematopoietic stem cells (HSCs), in vivo differentiated CD4+ T cells and CD19+ B cells as well as in vitro differentiated erythrocyte precursor cells, we identified hundreds of transcripts showing type-specific expression in these cell types. To understand the epigenomic changes related to tissue-specific expression during HSC differentiation, we examined the genome-wide distribution of H3K4me1, H3K4me3, H3K27me1, H3K27me3, histone variant H2A.Z, chromatin remodeler BRG1, and RNA Polymerase II in the same four cell types, as well as embryonic stem cells. Analysis of these datasets revealed that numerous key differentiation genes are primed for expression by Brg1 and Pol II binding, as well as bivalent modifications in the HSCs prior to their expression in downstream differentiated cell types. Much of this bivalency in HSC is retained from embryonic stem cells. After differentiation, these modified regions resolve to active chromatin modification configuration in the specific lineage, while in parallel differentiated lineages the bivalent modification remains; Pol II and Brg1 are lost in closer lineages but bivalency resolves to silent monovalency in more distant lineages. Correlation of tissue-specific gene expression with the epigenomic changes predicts tens of thousands of potential common enhancers and tissue-specific enhancers, which may critically contribute to the expression patterns. We provide a valuable dataset for further understanding the regulatory mechanisms of differentiation and function of blood lineages. This SuperSeries is composed of the SubSeries listed below. Refer to individual Series.

2013-03-25 | E-GEOD-39229 | biostudies-arrayexpress

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