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E-GEOD-55735

ABSTRACT: RNA-seq of mouse ES cells with conditional Drosha knockout against wild type controls to identify pri-miRNAs

OTHER RELATED OMICS DATASETS IN: PRJNA240848

PROVIDER: E-GEOD-55735 | ExpressionAtlas | 2019-05-14

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-GEOD-55735-analysis-methods.tsv	Tabular
	E-GEOD-55735-analytics.tsv	Tabular
	E-GEOD-55735-analytics.tsv.undecorated	Tabular
	E-GEOD-55735-analytics.tsv.undecorated.unrounded	Tabular
	E-GEOD-55735-analytics.tsv.unrounded	Tabular

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Project description:We report the ability of the Drosha null/conditional-null mouse model to enable the identification of pri-miRNA transcripts. The conditional-null allele of Drosha phenocopies the null allele both in mESC and in mice, upon conversion to the null state with Cre. Examination of the effects of Drosha deficiency in mouse embryonic stem cells.

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A quantitative map of human primary microRNA processing sites

Project description:Maturation of canonical microRNA (miRNA) is initiated by DROSHA that cleaves the primary transcript (pri-miRNA). Over 1,800 miRNA loci are annotated in humans, but it remains largely unknown if and at which sites the pri-miRNAs are cleaved by DROSHA. Here we performed in vitro processing on a full set of human pri-miRNAs (miRBase v21) followed by sequencing. This comprehensive profiling enabled us to classify miRNAs based on DROSHA-dependence and map their cleavage sites with respective processing efficiency measures. Only 758 pri-miRNAs are confidently processed by DROSHA, while the majority may be non-canonical or false entries. Analyses of the DROSHA-dependent pri-miRNAs show key cis-elements for processing. We observe widespread alternative processing as well as unproductive cleavage events such as “nick” or “inverse” processing. SRSF3 is a broad-acting auxiliary factor modulating alternative processing and suppressing unproductive processing. The profiling data and methods developed in this study will allow systematic analyses of miRNA regulation.

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