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DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [HiC]

ABSTRACT: DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [HiC]

PROVIDER: PRJNA419462 | ENA |

REPOSITORIES: ENA

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DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [HiC]

Project description:We present the high resolution HiC study of genome folding in primary cells, specifically hematopoietic stem and progenitor cells. We investigated the relationship of chromosomal contacts with other epigenetic marks, particularly DNA methylation and histone modifications which is known to be important for appropriate stem cell differentiation.

2017-11-24 | GSE107148 | GEO

DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells

Project description:DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells

| PRJNA413130 | ENA

DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [RNA-seq]

Project description:DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [RNA-seq]

| PRJNA419463 | ENA

DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [ChIP-seq]

Project description:DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [ChIP-seq]

| PRJNA419461 | ENA

DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [RNA-seq]

Project description:We present the high resolution HiC study of genome folding in primary hematopoietic stem and progenitor cells. We investigated the relationship of chromosomal contacts with other epigenetic marks, particularly DNA methylation which is known to be important for appropriate stem cell differentiation.

2017-11-24 | GSE107149 | GEO

DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [ChIP-seq]

2017-11-24 | GSE107147 | GEO

DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-11-24 | GSE104579 | GEO

R-loops induce repressive chromatin marks over mammalian gene terminators

Project description:The formation of R-loops is a natural consequence of the transcription process, caused by invasion of the DNA duplex by nascent transcripts. These structures have been considered rare transcriptional by-products with potential harmful effects on genome integrity, due to the fragility of the displaced DNA coding strand. However R-loops may also possess beneficial effects as their widespread formation has been detected over CpG island promoters in human genes. Furthermore we have previously shown that R-loops are particularly enriched over G-rich terminator elements. These facilitate RNA polymerase II (Pol II) pausing prior to efficient termination. Here we reveal an unanticipated link between R-loops and RNA interference (RNAi)-dependent H3K9me2 formation over pause site termination regions of mammalian protein coding genes. We show that R-loops induce antisense transcription over these pause elements which in turn lead to the generation of double-strand RNA (dsRNA) and recruitment of Dicer, Ago1, Ago2, and G9a histone lysine methyltransferase (HKMT). Consequently an H3K9me2 repressive mark is formed and Heterochromatin Protein 1γ (HP1γ) is recruited, that reinforces Pol II pausing prior to efficient transcriptional termination. We predict that R-loops promote a chromatin architecture that defines the termination region for a substantial subset of mammalian genes. PolIIS2ph ChIP-seq and input in untreated condition and treated with BIX and RNaseH1 overexpression in HeLa cells. The 4 samples have been multiplexed, pooled and sequenced on 3 lanes of Illumina HiSeq2000.

2014-09-29 | E-GEOD-59878 | biostudies-arrayexpress

Selective enhancement and repression of glucocorticoid receptor signaling by coregulator Hic-5

Project description:The glucocorticoid receptor (GR) recruits many coregulators via the well characterized AF2 interaction surface in the GR ligand binding domain, but LIM domain coregulator Hic-5 binds to the relatively uncharacterized tau2 activation domain in the hinge region of GR. Requirement of Hic-5 for glucocorticoid-regulated gene expression in U2OS osteosarcoma cells was defined by Hic-5 depletion and global gene expression analysis. Hic-5 depletion had selective and dramatic effects, positive and negative, on both activation and repression of GR target genes. For some hormone-induced genes, Hic-5 facilitated recruitment of the Mediator complex and RNA polymerase II. In contrast, many genes were not regulated by hormone until Hic-5 was depleted. On these genes Hic-5 acted at a very early step of the regulatory process, preventing efficient GR binding on enhancers, chromatin remodeling, and thus preventing glucocorticoid-driven transcriptional regulation. Overall, Hic-5 has selective and diverse roles on GR target genes, functioning as coactivator on some genes and corepressor on others, and either facilitating or opposing the glucocorticoid-driven actions of GR. Hic-5 exhibits multiple mechanisms of action, either regulating GR binding to DNA and chromatin remodeling, or facilitating later steps in transcription complex assembly. We investigate the relationship between GR and Hic5 and identify classes of genes that respond differently when cells are induced with hormone and when Hic5 is knocked down We knock down Hic-5 (TGFB1I1) in U2OS cells using siRNA (siHic5_2) along with nonspecific siRNA (shNS) and assay gene expression changes at 4 different time points of hormone treatment. We also include non-infected control (NI) as a second control at each time point.

2014-03-21 | E-GEOD-46448 | biostudies-arrayexpress

Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops

Project description:Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops

| PRJNA602661 | ENA