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Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly (PAR-CLIP)

ABSTRACT: Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly (PAR-CLIP)

PROVIDER: PRJNA471707 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7172042.fastq.gz	Fastqsanger.gz
	SRR7172043.fastq.gz	Fastqsanger.gz

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Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly (PAR-CLIP)

Project description:In S. pombe, transcripts derived from the pericentromeric dg and dh repeats promote heterochromatin formation via RNAi as well as an RNAi-independent mechanism involving the RNAPII-associated RNA-binding protein Seb1 and RNA processing activities. We show that Seb1 promotes long-lived RNAPII pauses at pericentromeric repeat regions and their presence correlates with the heterochromatin-triggering activities of the corresponding dg and dh DNA fragments. Globally increasing RNAPII stalling by other means induces the formation of novel large ectopic heterochromatin domains. Such ectopic heterochromatin occurs even in cells lacking RNAi. These results uncover Seb1-mediated polymerase stalling as a signal necessary for heterochromatin nucleation.

2018-07-03 | GSE114537 | GEO

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.

2022-10-18 | MSV000090547 | MassIVE

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2013-06-27 | E-GEOD-43909 | biostudies-arrayexpress

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Genes regulated by Hfq (PAR-CLIP)

Project description:Genes regulated by Hfq (PAR-CLIP)

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Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly

Project description:Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly

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YBX1 indirectly targets heterochromatin-repressed inflammatory response genes through binding to CBX5 [PAR-CLIP]

Project description:YBX1 indirectly targets heterochromatin-repressed inflammatory response genes through binding to CBX5 [PAR-CLIP]

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Advancing Functional Utility of PAR-CLIP by Quantifying Background Binding to mRNAs and lncRNAs

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