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RNA-Seq of control, RNPS1 knockdown and rescue in HeLa cells

ABSTRACT: RNA-Seq of control, RNPS1 knockdown and rescue in HeLa cells

PROVIDER: PRJEB25518 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2391650_1.fastq.gz	Fastqsanger.gz
	ERR2391650_2.fastq.gz	Fastqsanger.gz
	ERR2391651_1.fastq.gz	Fastqsanger.gz
	ERR2391651_2.fastq.gz	Fastqsanger.gz
	ERR2391652_1.fastq.gz	Fastqsanger.gz

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RNA-Seq of control, RNPS1 knockdown and rescue in HeLa cells

Project description:We report the knockdown and rescue of RNPS1, a component of the ASAP and PSAP complexes and, hence, an auxiliary component of the exon junction complex. The studied conditions show an extensive change in alternative splicing and the cell's transcriptome. For the knockdown, HeLa cells were transfected with siRNAs targeting RNPS1 or the Luciferase control. Total RNA was extracted with peqGOLD TriFast, underwent ribosomal depletion and strand-specific library preparation (TruSeq R Stranded Total RNA LT). Sequencing occurred in an Illumina HiSeq4000 sequencer with 2×75bp, producing roughly 35 million read-pair per sample.

2018-11-01 | E-MTAB-6564 | biostudies-arrayexpress

RNA-Seq of control and RNPS1 knockdown with or without RNPS1-RRM domain rescue in HeLa Tet-Off cells

Project description:RNPS1 is a splicing regulatory protein and a component of the ASAP/PSAP complex, which is associated with the exon junction complex and modulates alternative splicing. It was previously postulated that the isolated RRM domain of RNPS1 in complex with ASAP/PSAP is able to regulate certain alternative splicing events. We aimed to investigate in HeLa Tet-Off cells which alternative splicing events are rescued by the expression of the isolated RRM domain of RNPS1 in a RNPS1 knockdown background by using RNA-Seq analyses. The rescue construct was stably integrated into the genome using the PiggyBac transposon system. As controls, either Luciferase (Luc) siRNA was used or RNPS1 was knocked down without rescue.

2022-05-06 | E-MTAB-10768 | biostudies-arrayexpress

RNA-Seq of control and RNPS1 knockdown with or without RNPS1-RRM domain rescue in HeLa Tet-Off cells

Project description:RNA-Seq of control and RNPS1 knockdown with or without RNPS1-RRM domain rescue in HeLa Tet-Off cells

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RNA-Seq of control and RNPS1 knockdown with or without RNPS1 wildtype or RNPS1-RRM domain rescue in Flp-In T-REx 293 cells

Project description:RNPS1 is a splicing regulatory protein and a component of the ASAP/PSAP complex, which is associated with the exon junction complex and modulates alternative splicing. It was previously postulated that the isolated RRM domain of RNPS1 in complex with ASAP/PSAP is able to regulate certain alternative splicing events. We aimed to investigate in Flp-In T-REx 293 cells which alternative splicing events are rescued by the expression of the wild type RNPS1 or the isolated RRM domain of RNPS1 in a RNPS1 knockdown background by using RNA-Seq analyses. The rescue construct was stably integrated into the genome using the PiggyBac transposon system. As controls, either Luciferase (Luc) siRNA was used or RNPS1 was knocked down without rescue.

2022-05-06 | E-MTAB-10770 | biostudies-arrayexpress

RNA-Seq of control and RNPS1 knockdown with or without RNPS1 wildtype or RNPS1-RRM domain rescue in Flp-In T-REx 293 cells

Project description:RNA-Seq of control and RNPS1 knockdown with or without RNPS1 wildtype or RNPS1-RRM domain rescue in Flp-In T-REx 293 cells

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RNA-Seq of control and EJC factor (EIF4A3, RBM8A, MAGOH) knockdowns in part with EIF4A3 rescue in HeLa Tet-Off cells

Project description:The exon junction complex is involved in gene expression regulation on multiple co- and post-transcriptional levels. We aimed to investigate in HeLa Tet-Off cells which gene expression alterations can be observed upon knockdown of core EJC factors (EIF4A3, RBM8A and MAGOH) or upon EIF4A3 knockdown and rescue with EIF4A3 wild type construct by using RNA-Seq analyses. The rescue construct was stably integrated into the genome using the PiggyBac transposon system. As control Luciferase (Luc) siRNA was used.

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Human glioma cells: chronophin (CIN/PDXP) knockdown vs. control or rescue

Project description:Transcriptional profiling of human glioma cells to elucidate the role of chronophin (CIN/PDXP) for glioma pathogenesis three-condition experiment: control cells vs. knockdown and knockdown vs. rescue

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Insights into transcriptome surveillance and alternative splicing regulation by the EJC-associated splicing factor RNPS1

Project description:Alternative splicing of pre-mRNAs increases the potential for regulation and complexity of gene expression. The exon junction complex (EJC) and its associated splicing factor RNPS1 were recently shown to suppress mis-splicing resulting from the usage of cryptic and reconstituted 5’ and 3’ splice sites in the vicinity of the EJC. Here, we aimed to further investigate the mechanisms underlying splicing regulation by RNPS1. A transcriptome-wide analysis identified hundreds of splice events affected by the knockdown (KD) of RNPS1 in HeLa cells. These included alternative splice site usage as well as intron retention, exon skipping and inclusion. However, only a fraction of these RNPS1-dependent splice events was fully or partially rescued by the expression of the RNPS1 RRM. These results indicated that another domain of RNPS1 is involved in the regulation of the majority of splicing events. Deletion experiments revealed that the N-terminus and S-domain, and in particular the C-terminus of RNPS1 strongly regulate these events. Several splicing factors, including SR proteins and U1 snRNP components, were strongly reduced in the interactome of RNPS1 lacking the C terminus. We conclude that RNPS1 interacts with many splicing factors to direct the assembly of EJC-dependent and-independent splicing complexes.

2022-05-31 | PXD027251 | Pride

E-MTAB-6564

Project description:RNA-Seq of control, RNPS1 knockdown and rescue in HeLa cells

2025-01-23 | E-MTAB-6564 | ExpressionAtlas

UPF1-depleted HeLa cells - effect on physiological targets

Project description:Nonsense-mediated mRNA decay (NMD) is a molecular pathway of mRNA surveillance that ensures rapid degradation of mRNAs containing premature translation termination codons (PTCs) in eukaryotes. Originally, NMD was thought of as a quality control pathway that targets non-functional mRNAs arising from mutations and splicing errors. More recently, NMD has been shown to also regulate normal gene expression and NMD thus emerged as one of the key post-transcriptional mechanisms of gene regulation. We have now systematically analyzed the molecular mechanism of variable NMD efficiency and used different HeLa cell strains as a model system. The results of this analysis show that NMD efficiency can be remarkably variable and represents a stable characteristic of these strains. Low NMD efficiency is shown to be functionally related to the reduced abundance of the exon junction component RNPS1 in one of the HeLa strain analyzed. Furthermore, restoration of functional RNPS1 expression, but not of NMD-inactive mutant proteins, also restores efficient NMD in the RNPS1 deficient cell line. We conclude that cellular concentrations of RNPS1 modify NMD efficiency and propose that the cell type specific co-factor availability represents a novel principle that controls NMD. Keywords: NMD UPF1 knock down

2007-03-01 | GSE7009 | GEO

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