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RNAseq for finding splicing events in Arabidopsis prefoldin and lsm8 mutants in different environmental conditions

ABSTRACT: RNAseq for finding splicing events in Arabidopsis prefoldin and lsm8 mutants in different environmental conditions

PROVIDER: PRJNA513852 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8422200_1.fastq.gz	Fastqsanger.gz
	SRR8422200_2.fastq.gz	Fastqsanger.gz
	SRR8422210_1.fastq.gz	Fastqsanger.gz
	SRR8422210_2.fastq.gz	Fastqsanger.gz
	SRR8422220_1.fastq.gz	Fastqsanger.gz

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RNAseq for finding splicing events in Arabidopsis prefoldin and lsm8 mutants in different environmental conditions

Project description:This GEO submission includes RNAseq raw data (fastq) and processed data (using ASpli 1.6.0) from samples obtained in the wild type and the single prefoldin4 and lsm8 mutants in three different environmental conditions as well as in the triple prefoldin2 prefoldin4 prefoldin6 mutant growth in standard conditions.

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Project description:Prefoldin is a heterohexameric complex conserved from archaea to humans that plays a cochaperone role during the co-translational folding of actin and tubulin monomers. Additional functions of prefoldin have been described, including a positive contribution to transcription elongation and chromatin dynamics in yeast. Here we show that prefoldin perturbations provoked transcriptional alterations across the human genome. Severe pre-mRNA splicing defects were also detected, particularly after serum stimulation. We found impairment of co-transcriptional splicing during transcription elongation, which explains why the induction of long genes with a high number of introns was affected the most. We detected genome-wide prefoldin binding to transcribed genes and found that it correlated with the negative impact of prefoldin depletion on gene expression. Lack of prefoldin caused global decrease in Ser2 and Ser5 phosphorylation of the RNA polymerase II carboxy-terminal domain. It also reduced the recruitment of the CTD kinase CDK9 to transcribed genes, and the association of splicing factors PRP19 and U2AF65 to chromatin, which is known to depend on CTD phosphorylation. Altogether the reported results indicate that human prefoldin is able to act locally on the genome to modulate gene expression by influencing phosphorylation of elongating RNA polymerase II, and thereby regulating co-transcriptional splicing.

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2019-11-25 | PXD015848 | Pride

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