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Combinatorial mRNA Regulation by miRNAs and Pumilio proteins [CLIP-seq]

ABSTRACT: Combinatorial mRNA Regulation by miRNAs and Pumilio proteins [CLIP-seq]

PROVIDER: PRJNA434038 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6714560.fastq.gz	Fastqsanger.gz
	SRR6714570.fastq.gz	Fastqsanger.gz
	SRR6714561.fastq.gz	Fastqsanger.gz
	SRR6714571.fastq.gz	Fastqsanger.gz
	SRR6714562.fastq.gz	Fastqsanger.gz

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Combinatorial mRNA Regulation by miRNAs and Pumilio proteins

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Combinatorial mRNA Regulation by miRNAs and Pumilio proteins [CLIP-seq]

Project description:Approximately 1500 RNA-binding proteins (RBPs) profoundly impact mammalian cellular function by controlling distinct sets of transcripts, often using sequence-specific binding to 3′ untranslated regions (UTRs) to regulate mRNA stability and translation. Aside from their individual effects, higher-order combinatorial interactions between RBPs on specific mRNAs have been proposed to underpin the regulatory network. To assess the extent of such co-regulatory control, we took a global experimental approach followed by targeted validation to examine interactions between two well-characterized and highly conserved RBPs, Argonaute2 (AGO2) and Pumilio (PUM1 and PUM2). Transcriptome-wide changes in AGO2-mRNA binding upon PUM knockdown were quantified by CLIP-seq, and the presence of PUM binding on the same 3′ UTR corresponded with cooperative and antagonistic effects on AGO2 occupancy. In addition, PUM binding sites that overlap with AGO2 showed differential, weakened binding profiles upon abrogation of AGO2 association, indicative of cooperative interactions. In luciferase reporter validation of candidate 3′ UTR sites where AGO2 and PUM colocalized, three sites were identified to host antagonistic interactions, where PUM counteracts miRNA-guided repression. Interestingly, the binding sites for the two proteins are too far for potential antagonism due to steric hindrance, suggesting an alternate mechanism. Our data experimentally confirms the combinatorial regulatory model and indicates that the mostly repressive PUM proteins can change their behavior in a context-dependent manner. Overall, the approach underscores the importance of further elucidation of complex interactions between RBPs and their transcriptome-wide extent.

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Project description:In this study, we identified the transcriptome-wide direct RNA target sites of the entire family of Pumilio proteins in the budding yeast Saccharomyces cerevisiae by deep sequencing of RNA regions bound by each of six Pumilio proteins. As a family, the Pumilio proteins of yeast interact with over half of the entire transcriptome. Computational analysis of Pumilio target sites reveal striking differences in mRNA stability, gene set categories, and response to nutrient deprivation conditions based on features of Pumilio binding. Some of these features include variations in primary sequence motif and presence of predicted structured RNA hairpins. Puf6p also binds snoRNAs.

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