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Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression

ABSTRACT: Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression

PROVIDER: PRJNA851372 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19763815.fastq.gz	Fastqsanger.gz
	SRR19763816.fastq.gz	Fastqsanger.gz
	SRR19763817.fastq.gz	Fastqsanger.gz
	SRR19763818.fastq.gz	Fastqsanger.gz
	SRR19763819.fastq.gz	Fastqsanger.gz

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Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression [Human]

Project description:Most pre-messenger RNA (pre-mRNA) undergo extensive processing to create distinct transcripts from the same gene. One of these processes, alternative polyadenylation, involves over twenty proteins to bind and cleave the pre-mRNA at poly(A) sites that can lie within the 3' UTR, introns, or exons; this can modulate protein function, but the effect of choosing a site internal to the gene vs. within the 3' UTR remains unclear. Here we show that reduced expression of CPSF6, one of the proteins involved in site selection, derails development in both humans and zebrafish by causing a bidirectional shift in poly(A) site usage. CPSF6 insufficiency favors the use of intronic poly(A) sites in neuronal genes, reducing mRNA and protein abundance, but promotes 3' UTR site usage in cardiovascular and skeletal genes, upregulating mRNA and protein.These data thus provide a long-sought link between APA and gene expression and shows that poly(A) site selection influences development.

2023-01-15 | GSE206557 | GEO

Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression [Zebrafish]

Project description:Most pre-messenger RNA (pre-mRNA) undergo extensive processing to create distinct transcripts from the same gene. One of these processes, alternative polyadenylation, involves over twenty proteins to bind and cleave the pre-mRNA at poly(A) sites that can lie within the 3' UTR, introns, or exons; this can modulate protein function, but the effect of choosing a site internal to the gene vs. within the 3' UTR remains unclear. Here we show that reduced expression of CPSF6, one of the proteins involved in site selection, derails development in both humans and zebrafish by causing a bidirectional shift in poly(A) site usage. CPSF6 insufficiency favors the use of intronic poly(A) sites in neuronal genes, reducing mRNA and protein abundance, but promotes 3' UTR site usage in cardiovascular and skeletal genes, upregulating mRNA and protein.These data thus provides a long-sought link between APA and gene expression and shows that poly(A) site selection influences development.

2023-01-15 | GSE206558 | GEO

Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression [Human]

Project description:Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression [Human]

| PRJNA851383 | ENA

Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression [Zebrafish]

Project description:Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression [Zebrafish]

| PRJNA851381 | ENA

Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-01-13 | GSE206559 | GEO

Phosphorylation of CPSF6 RS-like domain

Project description:Cleavage factor I mammalian (CFIm) complex, composed of cleavage and polyadenylation specificity factor CPSF6, regulates alternative polyadenylation (APA). CPSF6 has a RS-like domain which plays role in protein -protein interactions. This interaction might have role in alternative polyadenylation site selection. The phosphorylation of RS- like domain might play role in protein -protein interaction and thus might have a role in alternative polyadenylation site selection. So we did mass specteroanalysis to analyse phosphorylation sites of RS-like domain of CPSF6.

2019-04-01 | PXD012713 | Pride

CPSF6 regulates alternative polyadenylation and proliferation of cancer cell through phase separation

Project description:In order to explore the impact of phase separation of CPSF6 on APA, we identified the structural domains that affect its phase separation formation and performed mutations. In addition, we also found that the phosphorylation of CPSF6 can also affect its phase separation effect, and identified key kinases. We performed IVT-SAPAS sequencing on both cases mentioned above.

2023-09-03 | GSE231823 | GEO

E3 ligase SYVN1-Mediated Polyubiquitination of CPSF6 Promotes Alternative Polyadenylation and Antivirus Effects of Macrophages

Project description:Down-regulation of CPSF6 protein, one of 3′ end processing factors, mediates APA in macrophage with responses to virus infection and plays an important role in its anti-virus effect. However, the signal pathway and molecular mechanism underlying the downregulation of the CPSF6 protein remain elusive. Here, we found that MAVS triggers the nucleus import of E3 ligase SYVN1 mediated by NUP153 in response to vesicular stomatitis virus infection. Then, SYVN1 catalyzes K48-linked polyubiquitination of CPSF6, resulting in the degradation of CPSF6 via proteasome, and then transcriptome wide APA and anti-virus effect subsequently.

2024-12-21 | GSE284508 | GEO

Alternative polyadenylation factor CPSF6 regulates temperature compensation of the mammalian circadian clock

Project description:A defining property of circadian clocks is temperature compensation, characterized by the resilience of circadian free-running periods against changes in environmental temperature.We quantify global changes in 3´UTR length as well as gene and protein expression between wild type and CPSF6 knock-down cells and their dependency on temperature.

2023-05-23 | PXD029343 | Pride

CPSF6 regulates alternative polyadenylation and proliferation of cancer cell through phase separation

Project description:CPSF6 regulates alternative polyadenylation and proliferation of cancer cell through phase separation

| PRJNA967743 | ENA