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A non-canonical R-loop resolving function of PIWIL4 maintains the genomic integrity and leukemic growth of AML cells [PAR-CLIP]

ABSTRACT: A non-canonical R-loop resolving function of PIWIL4 maintains the genomic integrity and leukemic growth of AML cells [PAR-CLIP]

PROVIDER: PRJNA778710 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16854267.fastq.gz	Fastqsanger.gz
	SRR16854268.fastq.gz	Fastqsanger.gz

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A non-canonical R-loop resolving function of PIWIL4 maintains the genomic integrity and leukemic growth of AML cells [PAR-CLIP]

Project description:PIWIL4 is a RNA binding enzyme required for the resolution of R-loops in AML cells. We examine the RNA associated with PIWIL4 protein in AML cell line THP-1

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A non-canonical R-loop resolving function of PIWIL4 maintains the genomic integrity and leukemic growth of AML cells

Project description:PIWIL4 enzyme is required for resolving R-loops and for growth of AML cells. We examine the impact of PIWIL4 knockdown and R-loop accumulation on gene expression in AML cell line THP-1

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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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Project description:AGO-PAR-CLIP was employed to identify microRNA binding sites in BCBL-1, a Kaposi's sarcoma-associated herpesvirus (KSHV) infected B-cell line and DG75, a KSHV negative B-cell line as a control. By using our novel computational method (PARma) and differential analysis of PAR-CLIP data, highly accurate target sites of KSHV microRNAs can be defined. Examination of microRNA target sites in two different cell lines using replicate PAR-CLIP experiments

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AGO-PAR-CLIP of DG75 and BCBL-1

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A non-canonical R-loop resolving function of PIWIL4 maintains the genomic integrity and leukemic growth of AML cells

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Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP

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