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Pseudouridylation is coupled with polyadenylation ot promote mRNA stability

ABSTRACT: Pseudouridylation is coupled with polyadenylation ot promote mRNA stability

PROVIDER: PRJNA764200 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15931130_1.fastq.gz	Fastqsanger.gz
	SRR15931130_2.fastq.gz	Fastqsanger.gz
	SRR15931131_1.fastq.gz	Fastqsanger.gz
	SRR15931131_2.fastq.gz	Fastqsanger.gz
	SRR15931132_1.fastq.gz	Fastqsanger.gz

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Pseudouridylation is coupled with polyadenylation ot promote mRNA stability

Project description:Here, we developed a Ψ RNA immunoprecipitation sequencing method (Ψ-RIP-seq) combined with direct RNA sequencing by Oxford Nanopore Technologies to detect mRNA Ψ transcriptome-wide. We identified a large number of novel Ψs in mRNA, revealing a conserved enrichment of Ψ in mRNA 3′ UTR. We further showed that a genome-wide association of Ψ with mRNA polyadenylation, and uncovered that cleavage factor complex I (CFI) regulated Ψ generation in mRNA 3′ UTR. We finally demonstrated that Ψ in mRNA 3′ UTR promoted mRNA stability in a CFI-dependent manner.

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Project description:Pseudo-seq was used to measure differences in the extent of pseudouridine (Î¨) modification in rRNA from mice haploinsufficient for the H/ACA biogenesis factor Naf1 compared to wild- type. We measured telomerase RNA levels as well as a sample of box H/ACA RNAs and found they were all decreased in Naf1+/- mice. Nevertheless, Naf1+/- mice had minimally decreased levels of pseudouridylation at the rRNA sites queried. This was not associated with any phenotypic abnormalities in vivo in these mice which we examined for hematopoeitic, liver, testes and brain defects. CMC treatment of RNA followed by next generation sequencing was used to measure the extent of pseudouridylation at mapped mouse rRNA Î¨ sites.

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Project description:mRNA stability plays an important role in gene expression. Here, using 3’ end sequencing of newly made and steady-state poly(A)+ RNAs, we compare transcript stability in multiple human cell lines, including HEK293T, HepG2, SH-SY5Y. We show that while mRNA stability is generally conserved across the cell lines, specific transcripts having high GC content and likely more stable secondary RNA structures are relatively more stable in SH-SY5Y cells compared to other two. These features also differentiate alternative polyadenylation (APA) 3’UTR isoforms in their stability difference in a cell type-specific manner. By analyzing cell differentiation of a neural stem cell line, we show that mRNA stability difference could contribute to gene expression changes in neurogenesis and confirms the neuronal identity of SH-SY5Y cells at gene expression and APA levels. Through comparison of APA isoforms, we show that mRNA stability control buffer the cleavage and polyadenylation site (PAS) choice in the cells studied. In addition, transcripts using intronic PAS are generally less stable, especially when the intron harboring the PAS is large and has a strong 5’ splice site, suggesting that intronic polyadenylation mostly plays a negative role in gene expression. Moreover, we found that poly(A)+ RNAs encoded by the mitochondrial genome are more stable in SH-SY5Y cells than the other two cell types, suggesting that mitochondrial RNA metabolism is distinct in neurons. Together, our results reveal multiple cell-specific mechanisms by which mRNA stability could contribute to the gene expression and APA programs that are important for cell identity.

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