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The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7 [PAR-CLIP]

ABSTRACT: The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7 [PAR-CLIP]

PROVIDER: PRJNA718535 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14108002_1.fastq.gz	Fastqsanger.gz
	SRR14108002_2.fastq.gz	Fastqsanger.gz
	SRR14108003_1.fastq.gz	Fastqsanger.gz
	SRR14108003_2.fastq.gz	Fastqsanger.gz
	SRR14108004_1.fastq.gz	Fastqsanger.gz

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The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7 [PAR-CLIP]

Project description:Chromodomain helicase DNA-binding protein 7 (Chd7) encodes an ATP-dependent chromatin remodeler required for normal human development. De novo mutations in CHD7 are the major cause of CHARGE syndrome which features multiple developmental defects. Previous studies have shown that CHD7 targets to specific genomic loci and alters local transcription potentially by remodeling the chromatin structure in a cell stage and lineage specific manner. We examined whether nuclear RNAs might contribute to its targeting and function. We used PAR-CLIP to identify a lncRNA, HERVH, that is uniquely expressed in pluripotent stem cells and preferentially interacts with CHD7. Knockdown of HERVH using LNAs or knockout of an individual copy of HERVH by CRISPR-Cas9 both resulted in increased binding of CHD7 and increased levels of H3K27ac at a subset of enhancers. Depletion of HERVH led to the activation of multiple genes, several of which might potentially poise cells towards differentiation. CHD7 bound HERVH RNA with high affinity but low specificity and that this interaction decreased the ability of CHD7 to bind and remodel nucleosomes. We present a model in which HERVH acts as a decoy to modulate the dynamics of CHD7 binding to enhancers in pluripotent cells and to prevent the activation of differentiation specific genes.

2021-10-10 | GSE171137 | GEO

The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7 [RNA-seq]

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The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7 [CUT&RUN]

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The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7 [ATAC-seq]

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The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7

Project description:The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7

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The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7 [ATAC-seq]

Project description:The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7 [ATAC-seq]

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The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7 [RNA-seq]

Project description:The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7 [RNA-seq]

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The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7 [CUT&RUN]

Project description:The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7 [CUT&RUN]

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Implementation of PAR-CLIP to characterize RNA-protein interactions in prokaryotes at nucleotide resolution

Project description:The identification of RNAs that are recognized by RNA-binding proteins (RNA-BPs) using techniques such as Crosslinking and Immunoprecipitation (CLIP) has revolutionized the genome-wide discovery of RNA-BP RNA targets. Among the different versions of CLIP that have been developed, the use of photoactivable nucleoside analogs has resulted in high efficiency photoactivable ribonucleoside-enhanced CLIP (PAR-CLIP) in vivo. Nonetheless, PAR-CLIP has not yet been applied in prokaryotes. To determine if PAR-CLIP can be used in prokaryotes, we determined suitable conditions for the incorporation of 4-thiouridine (4SU), a photoactivable nucleoside, into E. coli RNA and for the isolation of RNA crosslinked to RNA-BPs of interest. Applying this technique to Hfq, a well-characterized regulator of small RNA (sRNA)-messenger RNA (mRNA) interactions, we showed that PAR-CLIP identified most of the known sRNA targets of Hfq, as well as functionally relevant sites of Hfq-mRNA interactions at nucleotide resolution. Based on our findings, PAR-CLIP represents an improved method to identify both the RNAs and the specific regulatory sites that are recognized by RNA-BPs in prokaryotes.

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