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Context dependent Histone H3 Lysine 4 methylation is necessary for repression and is a requisite modification for facultative heterochromatin at distinct loci

ABSTRACT: Context dependent Histone H3 Lysine 4 methylation is necessary for repression and is a requisite modification for facultative heterochromatin at distinct loci

PROVIDER: PRJNA497111 | ENA |

REPOSITORIES: ENA

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Context dependent Histone H3 Lysine 4 methylation is necessary for repression and is a requisite modification for facultative heterochromatin at distinct loci [RNA-seq]

Project description:Context dependent Histone H3 Lysine 4 methylation is necessary for repression and is a requisite modification for facultative heterochromatin at distinct loci [RNA-seq]

| PRJNA497109 | ENA

Context dependent Histone H3 Lysine 4 methylation is necessary for repression and is a requisite modification for facultative heterochromatin at distinct loci [ChIP-seq]

Project description:Context dependent Histone H3 Lysine 4 methylation is necessary for repression and is a requisite modification for facultative heterochromatin at distinct loci [ChIP-seq]

| PRJNA497093 | ENA

Context dependent Histone H3 Lysine 4 methylation is necessary for repression and is a requisite modification for facultative heterochromatin at distinct loci

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

2018-11-30 | GSE121356 | GEO

Context dependent Histone H3 Lysine 4 methylation is necessary for repression and is a requisite modification for facultative heterochromatin at distinct loci [RNA-seq]

Project description:Sensing and responding to light provides organisms an adaptive advantage, in part by altering gene expression. The complement of light-activated genes in model organisms is largely known, and some of the mechanisms by which proteins modulate the light response are likewise well defined. However, how light alters post translation modifications to chromatin and how changes in chromatin facilitates and/or inhibit changes in gene expression has not been examined in depth. Nor is know how specific chromatin-modifiers assist in modulating the light response or the extent of the defects in strains lacking certain chromatin modifications. Using a combination of RNA-seq and ChIP-seq we examines H3K4 methylation and H3K9 methylation and found paradigm changing properties beyond the consensus that H3K4me3 is a solely a mark for activation and H3K9me3 marks silent heterochromatin domains.

2018-11-30 | GSE121353 | GEO

Context dependent Histone H3 Lysine 4 methylation is necessary for repression and is a requisite modification for facultative heterochromatin at distinct loci [ChIP-seq]

2018-11-30 | GSE121333 | GEO

Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci.

Project description: Not available

| S-EPMC6505117 | biostudies-literature

Context Dependency of Set1/COMPASS Mediated H3 Lysine 4 Trimethylation

Project description:The stimulation of trimethylation of histone H3 lysine 4 (H3K4) by H2B monoubiquitination (H2Bub) has been widely studied with multiple mechanisms proposed for this form of histone crosstalk. Cps35/Swd2 within COMPASS is considered to bridge these processes. However, a truncated form of Set1 (762-Set1) is reported to function in H3K4 trimethylation without interacting with Cps35/Swd2, and such crosstalk is attributed to the n-SET domain of Set1 and its interaction with the Cps40/Spp1 subunit of COMPASS. Here, we use biochemical, structural, in vivo, and ChIP-seq approaches to demonstrate that Cps40/Spp1 and the n-SET domain of Set1 are required for the stability of Set1 and not the crosstalk. Furthermore, the apparent wild-type levels of H3K4 trimethylation (H3K4me3) in the 762-Set1 strain is due to rogue methylase activity of this mutant resulting in the mislocalization of H3K4me3 from the promoter-proximal regions to gene bodies and intergenic regions. We have also performed detailed screens and identified yeast strains lacking H2Bub, but containing intact H2Bub enzymes, that have normal levels of H3K4me3, suggesting that ubiquitination may not directly stimulate COMPASS, but rather works in a context of the PAF and Rad6/Bre1 complexes. Our study demonstrates that the ubiquitination machinery and Cps35/Swd2 function to focus COMPASS’ H3K4me3 activity at promoter-proximal regions in a context dependent manner. ChIP-Seq for H3K4ME3 in S. cerevisie wild-type strains and strains expressing a truncated form of Set1: aa762-1080 Set1. H3K4ME3 ChIP-Seq was also compared for wild-type, leo1 knockout, and chd1 knockout strains

2014-01-09 | E-GEOD-53241 | biostudies-arrayexpress

Histone deacetylation promotes transcriptional silencing at facultative heterochromatin

Project description:It is important to accurately regulate the expression of genes involved in development and environmental response. In the fission yeast Schizosaccharomyces pombe, meiotic genes are tightly repressed during vegetative growth. Despite being embedded in heterochromatin these genes are transcribed and believed to be repressed primarily at the level of RNA. However, the mechanism of facultative heterochromatin formation and the interplay with transcription regulation is not understood. We show genome-wide that HDAC-dependent histone deacetylation is a major determinant in transcriptional silencing of facultative heterochromatin domains. Indeed, mutation of class I/II HDACs leads to increased transcription of meiotic genes and accumulation of their mRNAs. Mechanistic dissection of the pho1 gene where, in response to phosphate, transient facultative heterochromatin is established by overlapping lncRNA transcription shows that the Clr3 HDAC contributes to silencing independently of SHREC, but in an lncRNA-dependent manner. We propose that HDACs promote facultative heterochromatin by establishing alternative transcriptional silencing.

2018-03-19 | GSE108668 | GEO

Context Dependency of Set1/COMPASS Mediated H3 Lysine 4 Trimethylation

2014-01-09 | GSE53241 | GEO

Facultative protein selenation controls redox sensitivity, adipose tissue thermogenesis and obesity

Project description:Oxidation of cysteines by reactive oxygen species (ROS) initiates thermogenesis in brown and beige adipose tissues. Cellular selenols, where sulfur is replaced with selenium, exhibit enhanced reactivity with ROS. Here we developed a mass spectrometric method to interrogate incorporation of selenols into proteins. Unexpectedly, this approach revealed facultative incorporation of selenium into proteins that lack canonical encoding for selenium-containing amino acids. Selenium was selectively incorporated into regulatory sites on key metabolic proteins, including as selenocysteine replacing cysteine at position 253 in UCP1. Remarkably, dietary selenium supplementation elevated facultative incorporation into UCP1, elevated energy expenditure through thermogenic adipose tissue, and protected against obesity. Together, these findings reveal the existence of facultative protein selenation, which correlates with impacts on thermogenic adipocyte function.

2021-09-09 | PXD018225 | Pride

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