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Genome wide map of H3K27me3 histone mark remeains unaltered after silecing of lncRNA SCIRT

ABSTRACT: Genome wide map of H3K27me3 histone mark remeains unaltered after silecing of lncRNA SCIRT

PROVIDER: PRJNA561539 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10044637.fastq.gz	Fastqsanger.gz
	SRR10044638.fastq.gz	Fastqsanger.gz
	SRR10044639.fastq.gz	Fastqsanger.gz
	SRR10044640.fastq.gz	Fastqsanger.gz
	SRR10044641.fastq.gz	Fastqsanger.gz

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Genome wide map of H3K27me3 histone mark remeains unaltered after silecing of lncRNA SCIRT

Project description:We generated genome wide map of H3K27me3 histone mark in mammospheres where we silenced lncRNA SCIRT, PRC2 member EZH2. We discovered that upon silencing of lncRNA SCIRT and EZH2, the distribution of this histone mark does not change. This indicates that lncRNA SCIRT is important for EZH2 function that is independant of its activity as a histone methyltranspherase.

2021-02-23 | GSE136186 | GEO

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Project description:Repressive mark H3K27me3 in PRMT6 KO NT2/D1 cells

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CTCF induces histone variant incorporation, erases the H3K27me3 histone mark and opens chromatin.

Project description:Insulators functionally separate active chromatin domains from inactive ones. The insulator factor, CTCF, has been found to bind to boundaries and to mediate insulator function. CTCF binding sites are depleted for the histone modification H3K27me3 and are enriched for the histone variant H3.3. In order to determine whether demethylation of H3K27me3 and H3.3 incorporation are a requirement for CTCF binding at domain boundaries or whether CTCF causes these changes, we made use of the LacI DNA binding domain to control CTCF binding by the Lac inducer IPTG. Here we show that, in contrast to the related factor CTCFL, the N-terminus plus zinc finger domain of CTCF is sufficient to open compact chromatin rapidly. This is preceded by incorporation of the histone variant H3.3, which thereby removes the H3K27me3 mark. This demonstrates the causal role for CTCF in generating the chromatin features found at insulators. Thereby, spreading of a histone modification from one domain through the insulator into the neighbouring domain is inhibited.

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Project description:YFP-tagged primary spermatocytes were sorted by FACS, then ChIP together with microarray analysis was used to generate a genome-wide map for the H3K27me3 histone mark.

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Effect of LINC00899 depletion on histone mark enrichment in HeLa cells

Project description:LncRNAs represent a major transcriptional output of the human genome, but the function of many of these elements is unknown. In this experiment, we have used the ‘CUT&RUN’ technique to quantify the changes in histone mark enrichment across the genome upon depletion of the lncRNA LINC00899 in HeLa cells. LINC00899 is of interest as its depletion results in mitotic delay, suggesting a role in mitotic progression. The CUT&RUN procedure uses antibodies to target a nuclease to the relevant protein binding site, cleaving the surrounding DNA for sequencing and yielding output equivalent to that of ChIP-seq. This experiment contains 2 replicate batches where each batch contains a sample with LINC00899 knocked down by RNA interference (RNAi); a RNAi negative control; a sample with LINC00899 knocked down with locked nucleic acid antisense oligonucleotides (LNA); and a LNA negative control. This was performed using antibodies against H3K4me3, H3K27ac, H3K36me3 and H3K27me3, as well as an IgG (goat-derived anti-rabbit) control. All samples in each batch were generated at the same time. Within each batch, all CUT&RUN experiments with the same knockdown were performed on nuclei obtained from the same cell culture. Independent cell cultures were used for experiments with different knockdown or in different batches.

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Genome-wide profiling of trimethylated histone H3 lysine 27 (H3K27me3) in brm mutant seedlings and in wt seedlings

Project description:By using ChIP-seq, we found that loss of BRM activity in developing seedlings leads to ectopic and increased H3K27me3 deposition at several hundred genes, indicating the critical role of BRM in preventing the inappropriate deposition of this histone mark. Unexpectedly, BRM also facilitates PcG function at some PcG targets, suggesting the requirement for BRM in the deposition of this mark at certain PcG target genes. Examination of H3K27me3 in 14-day-old wt and brm seedlings. Two biological replicates for each one.

2014-03-01 | E-GEOD-47202 | biostudies-arrayexpress

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Project description:The regulatory effects of H3K27me3 on target genes expressions were analyzed by comparing S. aureus mastitis resistant and susceptible cows. The differentially expressed genes are mainly associated with immune and disease-related processes, which were negatively regulated by H3K27me3 modification on the up 2Kb regions relative to TSS in S. aureus mastitis cattle.

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Project description:Here we map the localization of H3K27me3 in Drosophila Kc cells, as well as in Drosophila Kc cells wherein dCTCF is knock down. examination of genomic occupancy for H3K27me3, control samples used for Drosophila Kc were previously described (Wood, Van Bortle et al., 2011 GSE30740)

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Genome-wide maps of the H3K27me3 histone modification in wild-type or SUZ12-mutant ipNF05.5 cells.

Project description:Using ChIP-seq, we profiled the H3K27me3 histone mark in wild-type or SUZ12-mutant ipNF05.5 cells.

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Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa (Illumina)

Project description:In higher eukaryotes, histone methylation is involved in the maintenance of cellular identity during somatic development. During spermatogenesis, Since most nucleosomes are replaced by protamines during spermatogenesis . Iit is therefore unclear whether if histone modifications function in paternal transmission of epigenetic information. Here we show that H3K4 di-methylation (H3K4me2) and H3K27 tri-methylation (H3K27me3), two modifications important for Trithorax and Polycomb-mediated gene regulation, display methylation-specific distributions at regulatory regions in human spermatozoa. H3K4 dimethylation H3K4me2-marksed promoters of genes relevant control gene functions in spermatogenesis and cellular homeostasis suggesting that this mark reflects germline transcription. In contrast, H3K27 trimethylation (H3K27me3) marks promoters of key developmental regulators in sperm like in somatic cells. Promoters of orthologous genes are similarly modified in mouse spermatozoa. Further, particularly genes with extensive H3K27me3 coverage around transcriptional start sites are never expressed during male and female gametogenesis, nor in pre-implantation embryos. These data are compatible with a function for Polycomb in repressing somatic determinants across generations. Importantly, however, we observe only modest selective retention of nucleosomes at regulatory regions in human sperm suggesting that paternal transmission of H3K27me3-encoded epigenetic information may be subjected to variegation. Identification of nucleosome containing regions in 6 human sperm samples

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