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Sequencing of liver RNA from HuR WT and HuR KO mice

ABSTRACT: Sequencing of liver RNA from HuR WT and HuR KO mice

PROVIDER: PRJNA600219 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10857525.fastq.gz	Fastqsanger.gz
	SRR10857526.fastq.gz	Fastqsanger.gz
	SRR10857527.fastq.gz	Fastqsanger.gz
	SRR10857528.fastq.gz	Fastqsanger.gz
	SRR10857529.fastq.gz	Fastqsanger.gz

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Sequencing of liver RNA from HuR WT and HuR KO mice

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Project description:Post-transcriptional regulatory networks are dependent on the interplay of many RNA-binding proteins having a major role in mRNA processing events in mammals. We have been interested in the concerted action of the two RNA-binding proteins hnRNP A1 and HuR, both stable components of immunoselected hnRNP complexes and having a major nuclear localization. Specifically, we present here the application of the RNA-immunoprecipitation (RIP)-Chip technology to identify a population of nuclear transcripts associated with hnRNP A1-RNPs as isolated from the nuclear extract of either HuR WT or HuR-depleted (KO) mouse embryonic fibroblast (MEF) cells. The outcome of this analysis was a list of target genes regulated via HuR for their association (either increased or reduced) with the nuclear hnRNP A1-RNP complexes. Real time PCR analysis was applied to validate a selected number of nuclear mRNA transcripts, as well as to identify pre-spliced transcripts (in addition to their mature mRNA counterpart) within the isolated nuclear hnRNP A1-RNPs. The differentially enriched mRNAs were found to belong to GO categories relevant to biological processes anticipated for hnRNP A1 and HuR (such as transport, transcription, translation, apoptosis and cell cycle) indicative of their concerted function in mRNA metabolism. Ribonucleoprotein Immunoprecipitation (RIP) using hnRNP A1 specific antibody was performed in nuclear extracts from HuR WT and HuR KO Mouse Embryonic Fibroblasts (MEFs). RNA isolated from these IPs together with nuclear RNA from the two cell types, was subjected to microarray analysis. Three biological replicates, representing three independent experiments, are available for each condition except in the case of nuclear RNA isolated from HuR WT MEFs that one replicate didn’t pass the quality control.

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Project description:iTRAQ proteomics was performed for Liver samples from WT and Atg7 liver specific KO mice

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