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PAR-CLIP of Slf1 and Sro9 during optimal growth and oxidative stress

ABSTRACT: PAR-CLIP of Slf1 and Sro9 during optimal growth and oxidative stress

PROVIDER: PRJNA731161 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR14588900_1.fastq.gz	Fastqsanger.gz
	SRR14588900_2.fastq.gz	Fastqsanger.gz
	SRR14588901_1.fastq.gz	Fastqsanger.gz
	SRR14588901_2.fastq.gz	Fastqsanger.gz
	SRR14588902_1.fastq.gz	Fastqsanger.gz

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PAR-CLIP of Slf1 and Sro9 during optimal growth and oxidative stress

Project description:We quantified the binding sites of the La related RNA-binding proteins Slf1 and Sro9 within RNAs using PAR-CLIP. Datasets were obtained for yeast cells during optimal growth and during the cellular response to peroxide stress.

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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:Genes regulated by Hfq (PAR-CLIP)

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Project description:We developed a method for measuring non-specific background in PAR-CLIP data demonstrating that covalently crosslinked background binding is common, reproducible and apparently universal. Furthermore, we show that quantitative determination of background is essential for identifying targets of weakly binding RNA-binding proteins and can substantially improve motif analysis. To define background binding events in PAR-CLIP data we performed the standard PAR-CLIP protocol (Hafner et al., Cell 2010.) on lysates expressing a commonly used non-RBP control, FLAG-GFP. After FLAG-tag immunopurification of UV 365nm irradiated lysates prepared from cells supplemented with 4-thiouridine (4SU), RNA was partially digested with RNase T1, radiolabeled and separated by SDS-PAGE. Reads were sequenced by Illumina HiSeq. PAR-CLIP was also performed for HuR. Included as well is a total from lysates treated like PAR-CLIP, but without immunoprecipitation (see sample description for more detail).

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