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Identification of candidate enhancer elements in unstimulated and stimulated dendritic cells and fibroblasts

ABSTRACT: To identify candidate enhancer elements we analyzed the distribution of two histone modifications associated with enhancers - H3K4me1 and H3K27ac - and one histone modification associated with active transcription - H4 acetylation. ChIP-seq for H3K4me1, H3K27ac and H4ac, and input DNA controls, from 2 cell types (DCs & fibroblasts) under 2 conditions (unstimulated & stimulated)

ORGANISM(S): Mus musculus

SUBMITTER: Dominic van Essen

PROVIDER: E-GEOD-32380 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Cell-type-specific control of enhancer activity by H3K9 trimethylation.

Zhu Yina Y van Essen Dominic D Saccani Simona S

Molecular cell 20120501 4

Cell-type-specific control of gene expression is critical for the development of multicellular organisms. To investigate the mechanisms which underlie this, we have studied the regulation of the model genes Mdc and Il12b, whose stimulus-induced expression is tightly restricted to specific cells of the immune system. Surprisingly, we find that neither the promoter nor the enhancer sequences of these genes are sufficient to direct this cell-type specificity. Instead, the activities of upstream enh ...[more]

PMID: 22633489

Similar Datasets

Cell-type specific control of enhancer activity by H3K9 trimethylation

Project description:This SuperSeries is composed of the following subset Series: GSE32255: JmjD2d-dependence of LPS-induced genes GSE32377: Analysis of H3K9 trimethylation in unstimulated and stimulated dendritic cells and fibroblasts GSE32379: Analysis of JmjD2d-bound regions in unstimulated and stimulated dendritic cells GSE32380: Identification of candidate enhancer elements in unstimulated and stimulated dendritic cells and fibroblasts Refer to individual Series

2012-05-27 | E-GEOD-32381 | biostudies-arrayexpress

Analysis of JmjD2d-bound regions in unstimulated and stimulated dendritic cells

Project description:To examine JmjD2d-binding, ChIP was performed using monoclonal antibodies specific for JmjD2d, or for the JmjN domain of all JmjD2-family members. ChIP-seq for JmjD2d, Jmjd2-family, and input DNA controls, from dendritic cells under 2 conditions (unstimulated & stimulated)

2012-11-19 | E-GEOD-32379 | biostudies-arrayexpress

Analysis of H3K9 trimethylation in unstimulated and stimulated dendritic cells and fibroblasts

Project description:The distribution of H3K9me3 was analyzed in order to investigate the influence of H3K9me3 levels surrounding candidate enhancers and other cis-regulatory elements. ChIP-seq for H3K9me3 and input DNA controls, from 2 cell types (DCs & fibroblasts) under 2 conditions (unstimulated & stimulated)

2012-11-19 | E-GEOD-32377 | biostudies-arrayexpress

H3K4me1 ChIP-seq of untreated HeLa S3 cells

Project description:We used ATLAS-seq to map the sites of integration of an engineered LINE-1 (L1) retrotransposon into the genome of HeLa S3 cells. Then, we compared the position of these sites with publicly available genomic datasets. In order to cross-corroborate our findings with datasets obtained in the same cell stock as used in our retrotransposition assays, we also performed H3K4me1 ChIP-seq.

2019-04-04 | E-MTAB-7643 | biostudies-arrayexpress

A role for H3K4 mono-methylation in facultative heterochromatin assembly and partitioning of chromatin readers

Project description:Mono-methylation of lysine 4 on histone H3 (H3K4me1) is a well-established feature of enhancers and promoters, although its function is unknown. Remarkably, we find H3K4me1 at the promoter regions of conditionaly-repressed muscle and stimulus-dependent inflammatory response genes in myoblasts. During myogenesis, muscle genes are activated and become H3K4-trimethylated. On the promoters of active genes, we find that H3K4me1 spatially restricts the recruitment of “readers” of H3K4me3, including ING1, which, in turn, recruits Sin3A. Our findings point to a unique role for H3K4 mono-methylation in establishing boundaries that restrict the recruitment of chromatin-modifying enzymes to defined regions within promoters. Mapping of Wdr5, Menin, MLL1, Sin3A, and LSD1 in growing myoblasts (MB) and ING1 in growing myoblasts (MB) and fully differentiated myotubes (MT).

2014-03-29 | E-GEOD-50590 | biostudies-arrayexpress

High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells

Project description:We describe the use of a novel DNA modification-dependent restriction endonuclease AbaSI coupled with sequencing (Aba-seq) to map high-resolution hydroxymethylome of mouse E14 embryonic stem cells. The specificity of AbaSI enables sensitive detection of 5hmC at low occupancy regions. Bioinformatic analysis suggests 5hmCs in genic regions closely follows the 5mC distribution. 5hmC is generally depleted in CpG islands and only enriched in a small set of repetitive elements. A regularly spaced and oscillating 5hmC pattern was observed at the binding sites of CTCF. 5hmC is enriched at the poised enhancers with the mono-methylated histone H3 lysine 4 (H3K4me1) marks, but not at the active enhancers with the acetylated histone H3 lysine 27 (H3K27Ac) marks. Non-CG hydroxymethylation appears to be prevalent in the mitochondrial genome. We propose that some amounts of transiently stable 5hmCs may indicate a poised epigenetic state or de-methylation intermediate, while others may suggest a locally accessible chromosomal environment to the TET enzymatic apparatus. Mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cell by enzymatic digistion of AbaSI coupled with high-throughput sequencing, in replicates.

2013-01-01 | E-GEOD-42898 | biostudies-arrayexpress

Genome-wide analysis of H3K4me1 in Lsh-/- mouse embryonic fibroblasts

Project description:We report here differentiated enrichment of H3K4me1 at Lsh WT and KO mouse embryonic fibroblasts (MEFs). We found a subset of differentially enriched H3K4me1 regions in Lsh KO MEFs, and they clustered at neuronal lineage genes and overlapping with known cis-regulatory elements present in brain tissue. Reprogramming of Lsh?/? MEFs into induced pluripotent stem (iPS) cells leads to increased neuronal lineage gene expression of premarked genes and enhanced differentiation potential of Lsh?/? iPS cells toward the neuronal lineage pathway compared with WT iPS cells in vitro and in vivo. The state of H3K4me1 enrichment is partially maintained in Lsh?/? iPS cells, suggesting the regions are preserved as potential enhancers. Genome-wide maps of H3K4me1 in Lsh WT and KO primary MEFs.

2014-03-25 | E-GEOD-56151 | biostudies-arrayexpress

Nucleosome occupancy dynamics in yeast BY4741 responding to 0.4mM H2O2 over time (0-60 min)

Project description:Numerous factors have been implicated in regulating gene expression changes, including changes to nucleosome occupancy. Here we followed dynamic changes to nucleosome occupancy, gene expression and DNA binding of the transcription factor Msn2p genome-wide in yeast cells responding to hydrogen peroxide to reveal new relationships between regulators of stress-dependent gene expression. Nucleosome occupancy was measured by MNase-Seq in response to .4mM H2O2 in the S288c yeast derivative BY4741. A single replicate was performed for the time-course experiment with time points at 0, 4, 12, 20, 40 and 60 minutes after treatment.

2012-06-18 | E-GEOD-30900 | biostudies-arrayexpress

Genome-wide maps of Runx3 bound regions in splenic NK cells

Project description:ChIP-seq was conducted using freshly isolated (resting) splenic WT NK cells with anti-Runx3 antibody (Ab), anti-H3K4me1 Ab and non-immune serum (NIS) as control. Runx3 and H3K4me1 IP from splenic NK cells isolated by negative selection using NK cell isolation kit (R&D) followed by sorting of NKp46+ cells.

2013-11-18 | E-GEOD-50127 | biostudies-arrayexpress

Genome-wide maps of chromatin state in mouse erythroid cells.

Project description:We generated genome-wide chromatin state and RNA Polymerase II binding maps in mouse erythroid cells by ChIP-Seq. Examination of 4 different histone modifications (H3K4me3, H3K4me1, H3K27me3, H3K27ac) and RNA Polymerase II (RNAP2) binding in mouse erythroid cells (Ter119+).

2012-01-30 | E-GEOD-27918 | biostudies-arrayexpress

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