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

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

PROVIDER: PRJNA419461 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6308420_1.fastq.gz	Fastqsanger.gz
	SRR6308420_2.fastq.gz	Fastqsanger.gz
	SRR6308421_1.fastq.gz	Fastqsanger.gz
	SRR6308421_2.fastq.gz	Fastqsanger.gz
	SRR6308417_1.fastq.gz	Fastqsanger.gz

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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

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

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

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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]

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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.

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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.

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

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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.

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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.

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AAV-mediated genome editing is influenced by the formation of R-loops.

Project description:Recombinant adeno-associated viral vectors (rAAV) hold a natural ability to stimulate homologous recombination (AAV-HR). Moreover, they are also reported to randomly integrate into numerous locations throughout the genome. Here, we describe DNA/RNA immune precipitation sequencing (DRIP-seq) studies in HEPA1-6 cells and whole murine liver to detect genomic r-loops. Through genetic and pharmacological manipulation of r-loops formation, we showed a significant enhancement of AAV-HR. Notably, we were able to detect different levels of r-loops along the Albumin locus. Both in vitro and in vivo experiments showed that the 3’ end of Albumin (high r-loops) is efficiently edited by AAV-HR, whereas the upstream region (low r-loops) did not result in any detectable vector integration. In addition, we were also able to find an interesting correlation between previously reported off-target rAAV integration and r-loop enriched genomic regions. Thus, we conclude that highly transcribed genes accumulate high levels of r-loops, and this could lead to rAAV vector genome integration. These findings may shed light on mechanisms for improving the safety and efficacy of genome editing and may enhance our ability to predict regions most susceptible to insertional mutagenesis with canonical rAAV vectors.

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ZNF143 mediates CTCF-bound promoter-enhancer loops required for murine hematopoietic stem and progenitor cell function

Project description:CCCTC binding factor (CTCF) is an important factor in the maintenance of chromatin chromatin interactions, yet the mechanism regulating its binding to chromatin is unknown. We demonstrate that zinc finger protein 143 (ZNF143) is a key regulator for CTCF bound promoter enhancer loops. In the murine genome, a large percentage of CTCF and ZNF143 DNA binding motifs are distributed 37 bp apart in the convergent orientation. Furthermore, deletion of ZNF143 leads to loss of CTCF binding on promoter and enhancer regions associated with gene expression changes. CTCF bound promoter enhancer loops are also disrupted after excision of ZNF143. ZNF143 CTCF bound promoter enhancer loops regulate gene expression patterns essential for maintenance of murine hematopoietic stem and progenitor cell integrity. Our data suggest a common feature of gene regulation that ZNF143 is a critical factor for CTCF bound promoter enhancer loops.

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