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Identification of different transcripts that favor the nuclear or cytoplasmic Poly(A) Binding Proteins (PABPs) through RNA immunoprecipitation

ABSTRACT: Identification of different transcripts that favor the nuclear or cytoplasmic Poly(A) Binding Proteins (PABPs) through RNA immunoprecipitation

PROVIDER: PRJNA800801 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17771363.fastq.gz	Fastqsanger.gz
	SRR17771364.fastq.gz	Fastqsanger.gz
	SRR17771365.fastq.gz	Fastqsanger.gz
	SRR17771366.fastq.gz	Fastqsanger.gz
	SRR17771367.fastq.gz	Fastqsanger.gz

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Identification of different transcripts that favor the nuclear or cytoplasmic Poly(A) Binding Proteins (PABPs) through RNA immunoprecipitation

Project description:The poly(A) tail appended to the 3’ end of many eukaryotic transcripts plays a key role in the stability, nuclear transport, and translation of the RNA. These roles are largely mediated by the Poly(A) Binding Proteins (PABPs) that coat the poly(A) tails and interact with various proteins involved in the biogenesis and function of the RNA. While it is well established that the nuclear PABP (PABPN) binds newly synthesized poly(A) tails and is apparently replaced by the cytoplasmic PABP (PABPC) on transcripts exported to the cytoplasm, the distribution of transcripts for different genes or isoforms of the same gene on these distinct PABPs has not been investigated on a genome-wide scale. Here, we analyzed the identity, splicing status, poly(A) tail size, and translation status of RNAs co-immunoprecipitated with endogenous PABPN or PABPC in human cells. At steady state, many protein coding and non-coding RNAs exhibit strong bias for association with PABPN or PABPC. While PABPN-enriched transcripts more often were incompletely spliced and harbored longer poly(A) tails and PABPC-enriched RNAs tended to have longer half-lives and higher translation efficiency, there are curious outliers. Overall, our study reveals the landscape of RNAs bound by PABPN and PABPC, providing new details that support and advance the current understanding of the roles these proteins play in poly(A) tail synthesis, maintenance and function.

2022-03-30 | GSE195495 | GEO

Nuclear and cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms.

Project description:The poly(A)-tail appended to the 3'-end of most eukaryotic transcripts plays a key role in their stability, nuclear transport, and translation. These roles are largely mediated by Poly(A) Binding Proteins (PABPs) that coat poly(A)-tails and interact with various proteins involved in the biogenesis and function of RNA. While it is well-established that the nuclear PABP (PABPN) binds newly synthesized poly(A)-tails and is replaced by the cytoplasmic PABP (PABPC) on transcripts exported to the cytoplasm, the distribution of transcripts for different genes or isoforms of the same gene on these PABPs has not been investigated on a genome-wide scale. Here, we analyzed the identity, splicing status, poly(A)-tail size, and translation status of RNAs co-immunoprecipitated with endogenous PABPN or PABPC in human cells. At steady state, many protein-coding and non-coding RNAs exhibit strong bias for association with PABPN or PABPC. While PABPN-enriched transcripts more often were incompletely spliced and harbored longer poly(A)-tails and PABPC-enriched RNAs had longer half-lives and higher translation efficiency, there are curious outliers. Overall, our study reveals the landscape of RNAs bound by PABPN and PABPC, providing new details that support and advance the current understanding of the roles these proteins play in poly(A)-tail synthesis, maintenance, and function.

| S-EPMC9071453 | biostudies-literature

RNA sequencing of synaptic and cytoplasmic Upf1-bound transcripts supports contribution of nonsense-mediated decay to epileptogenesis

Project description:Immunoprecipitation of Upf1-bound RNA from the cytoplasmic and synaptosomal compartments followed by RNA sequencing identified unique populations of NMD-associated transcripts and altered levels after status epilepticus.

2016-12-06 | GSE90870 | GEO

The cytoplasmic poly(A) polymerases GLD-2 and GLD-4 promote general gene expression via distinct mechanisms

Project description:Comparision of mRNA abundance and translation efficiency mediated by cytoplasmic poly(A) polymerases in C. elegans

2014-10-02 | GSE58918 | GEO

The cytoplasmic poly(A) polymerases GLD-2 and GLD-4 promote general gene expression via distinct mechanisms

Project description:Comparision of mRNA abundance and translation efficiency mediated by cytoplasmic poly(A) polymerases in C. elegans comparision of different adults treated with RNAi

2014-10-02 | E-GEOD-58918 | biostudies-arrayexpress

RNA immunoprecipitation to identify RHA-binding transcripts in HEK293 cells

Project description:Given that RHA regulates translation by binding a PCE located at the 5’ UTR of the target transcripts a genome-wide screen was performed to identify mRNAs that bind RHA in vivo. The results from four experiments with samples obtained in four independent RNA immunoprecipitations identified 375 transcripts that co-immunoprecipitate with FLAG RHA. Since N-terminal FLAG tagged RHA specifically co-immunoprecipitates PCE-containing mRNAs HEK293 cells were transfected with a CMV-FLAG-RHA construct. Cytoplasmic lysates were immunoprecipitated with anti-FLAG beads. RNA was extracted from the immunoprecipitate and used to probe a human Agilent expression arrays. An immunoprecipitation with cells transfected with empty FLAG plasmid was used as negative control.

2010-08-19 | E-GEOD-23688 | biostudies-arrayexpress

Cytoplasmic and nuclear fractionation from HEK293T cells

2022-03-30 | GSE195493 | GEO

Ataxin-2, Twenty-four and Dicer-2 are components of a non-canonical cytoplasmic polyadenylation complex

Project description:Cytoplasmic polyadenylation is a mechanism to promote mRNA translation in a wide variety of biological contexts. A canonical complex centered around the conserved RNA-binding protein family CPEB has been shown to be responsible for this process. We have previously reported evidence for an alternative non-canonical, CPEB-independent complex in Drosophila, of which the RNA-interference factor Dicer-2 is a component. Here, we investigate Dicer-2 mRNA targets and protein co-factors in cytoplasmic polyadenylation. Using RIP-Seq analysis we identify hundreds of novel Dicer-2 target transcripts, ~50% of which were previously found as targets of the cytoplasmic poly(A) polymerase Wispy, suggesting widespread roles of Dicer-2 in cytoplasmic polyadenylation. Large-scale immunoprecipitation revealed Ataxin-2 and Twenty-four among the high-confidence interactors of Dicer-2. Functional analysis indicate that both factors form an RNA-independent complex with Dicer-2, and are required for cytoplasmic polyadenylation of Dicer-2 targets. Our results reveal the composition of a novel cytoplasmic polyadenylation complex that operates during Drosophila early embryogenesis.

2022-08-29 | GSE189868 | GEO

Identification of mRNAs enriched in G3BP immunoprecipitation

Project description:A phosphorylation-dependent endoribonuclease G3BP localizes in cytoplasmic stress granules (SGs). G3BP promotes SG assembly, oligomerizes, binds mRNA, and regulates levels of certain mRNAs. Transcripts bound to G3BP were identified through expression profiling of a total of 12,135 genes by immunoprecipitation (IP) with anti-G3BP or control IgG from S2-013 cells, converting the immunoprecipitated transcripts to cDNA by reverse transcription, and hybridizing these products to cDNA microarrays. Five G3BP-associated transcripts were identified.

2009-07-23 | GSE17056 | GEO

TENT5A mediated cytoplasmic polyadenylation in osteoblast supports proper bone formation.

Project description:The bone formation, osteogenesis, is a very complex process in which osteoblasts play a crucial role. The primary function of theses terminally differentiated mesenchymal stem cells is the secretion of fibrillary, dense, highly crosslinked type 1 collagen. Herein we show that the TENT5A gene, which mutations lead to osteogenesis imperfecta, is an active cytoplasmic poly(A) polymerase, which in osteoblast positively regulates the expression of collagen subunits and also other secreted proteins essential for proper bone formation. TENT5A substrates have shorter poly(A) tails in TENT5 KO, as revealed by direct RNA sequencing. In the case of Col1α1 and Col1α2 transcripts, the lack of cytoplasmic polyadenylation by TENT5 leads to drastic decree in the protein production but also aberrant structure. The increase in TENT5A expressing during osteoblasts differentiation positively correlates with the cytoplasmic extension of the poly(A) trials of mRNA targets. The first physiologically relevant regulation of collagen expression at the posttranscriptional level.

2022-02-16 | PXD020346 | Pride

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