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Genome-wide analysis of cellular NMD substrates that regulated by Upf1, PNRC2 or CTIF in HeLa cell

ABSTRACT: The first round of translation occurs on mRNAs bound by nuclear cap-binding complex (CBC), which is composed of nuclear cap-binding protein (CBP) 80 and 20. During this round of translation, aberrant mRNAs are recognized and downregulated in abundance by nonsense-mediated mRNA decay (NMD), which is one of the mRNA quality control mechanisms. Here our microarray analysis reveals that the level of cyclin-dependent kinase inhibitor 1A (CDKN1A) mRNAs increases in the cells depleted of cellular NMD factors. Intriguingly, CDKN1A mRNA contains an upstream open reading frame (uORF), which is one of NMD-inducing features. Using chimeric reporter constructs and confocal microscopy, we find that the uORF of CDKN1A mRNA is actively translated and modulates a translational efficiency of the main downstream ORF. Our findings provide the biological insights into the possible role of NMD in diverse pathways mediated by CDKN1A. The microarray analysis performed to analize the cellular NMD substrates that regulated by Upf1, PNRC2 and/or CTIF in HeLa cell. The hypothesis tested in the present study was that endogenous NMD substrates may co-regulated by Upf1, PNRC2 and CTIF. Results provide important information that vast range of cellular NMD substrates are reqired CTIF.

ORGANISM(S): Homo sapiens

PROVIDER: GSE37538 | GEO | 2012/07/23

SECONDARY ACCESSION(S): PRJNA161531

REPOSITORIES: GEO

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Genome-wide analysis of cellular NMD substrates that regulated by Upf1, PNRC2 or CTIF in HeLa cell

Project description:The first round of translation occurs on mRNAs bound by nuclear cap-binding complex (CBC), which is composed of nuclear cap-binding protein (CBP) 80 and 20. During this round of translation, aberrant mRNAs are recognized and downregulated in abundance by nonsense-mediated mRNA decay (NMD), which is one of the mRNA quality control mechanisms. Here our microarray analysis reveals that the level of cyclin-dependent kinase inhibitor 1A (CDKN1A) mRNAs increases in the cells depleted of cellular NMD factors. Intriguingly, CDKN1A mRNA contains an upstream open reading frame (uORF), which is one of NMD-inducing features. Using chimeric reporter constructs and confocal microscopy, we find that the uORF of CDKN1A mRNA is actively translated and modulates a translational efficiency of the main downstream ORF. Our findings provide the biological insights into the possible role of NMD in diverse pathways mediated by CDKN1A. The microarray analysis performed to analize the cellular NMD substrates that regulated by Upf1, PNRC2 and/or CTIF in HeLa cell. The hypothesis tested in the present study was that endogenous NMD substrates may co-regulated by Upf1, PNRC2 and CTIF. Results provide important information that vast range of cellular NMD substrates are reqired CTIF. Total RNA obtained from HeLa cells with downregulation of Upf1, PNRC2 or CTIF by siRNA. The up- or down-regulated transcripts were compare to control siRNA treated HeLa cell RNA extract. Significant transcripts were confirmed by replication.

2012-07-22 | E-GEOD-37538 | biostudies-arrayexpress

A post-translational regulatory switch on UPF1 controls targeted mRNA degradation.

Project description:Nonsense-mediated mRNA decay (NMD) controls the quality of eukaryotic gene expression and also degrades physiologic mRNAs. How NMD targets are identified is incompletely understood. A central NMD factor is the ATP-dependent RNA helicase UPF1. Neither the distance in space between the termination codon and the poly(A) tail nor the binding of steady-state, largely hypophosphorylated UPF1 is a discriminating marker of cellular NMD targets, unlike for PTC-containing reporter mRNAs when compared to their PTC-free counterparts. Here, we map phosphorylated UPF1 (p-UPF1) binding sites using transcriptome-wide footprinting or DNA oligonucleotide-directed mRNA cleavage to report that p-UPF1 provides the first reliable cellular NMD-target marker. p-UPF1 is enriched on NMD target 3'UTRs along with SMG5 and SMG7 but not SMG1 or SMG6. Immunoprecipitations of UPF1 variants deficient in various aspects of the NMD process in parallel with FRET experiments reveal that ATPase/helicase-deficient UPF1 manifests high levels of RNA binding and disregulated hyperphosphorylation, whereas wild-type UPF1 releases from nonspecific RNA interactions in an ATP hydrolysis-dependent mechanism until an NMD target is identified. 3'UTR-associated UPF1 undergoes regulated phosphorylation on NMD targets, providing a binding platform for mRNA degradative activities. p-UPF1 binding to NMD target 3'UTRs is stabilized by SMG5 and SMG7. Our results help to explain why steady-state UPF1 binding is not a marker for cellular NMD substrates and how this binding is transformed to induce mRNA decay.

2014-08-15 | GSE60045 | GEO

A post-translational regulatory switch on UPF1 controls targeted mRNA degradation.

2014-08-15 | E-GEOD-60045 | biostudies-arrayexpress

Genome-wide analysis of miRNA-targeted cellular NMD substrates in HeLa cell

Project description:Analysis of miRNA-targeted cellular NMD substrates in HeLa cell. The hypothesis tested in the present study was that endogenous NMD substrates containing long 3' untranslated region may targeted for miRNA. Results provide important information expanding the roles of miRISC in the posttranscriptional regulation of gene expression: a new cross-talk between miRNA-mediated gene silencing and NMD. ABSTRACT: Imperfect base-pairing between microRNA (miRNA) and the 3â-untranslated region (3âUTR) of target mRNA triggers translational repression of the target mRNA. Here, we provide evidence that human Argonaute 2 (Ago2) targets cap-binding protein (CBP)80/20- and exon junction complex (EJC)-bound mRNAs and inhibits nonsense-mediated mRNA decay (NMD), which is tightly restricted to CBP80/20-bound mRNAs. Furthermore, microarray analyses reveal that a subset of cellular transcripts, which are expected to be targeted for NMD, is stabilized by miRNA-mediated gene silencing. The regulation of NMD by miRNAs will shed light on a new post-transcriptional regulation mechanism of gene expression in mammalian cells Total RNA obtained from HeLa cells with downregulation of Ago2 or Ago2/UPF1 by siRNA. The up- or down-regulated transcripts were compared to control siRNA treated HeLa cell RNA extract. Significant transcripts were confirmed by replication.

2010-04-09 | E-GEOD-16170 | biostudies-arrayexpress

Regulated endocleavage balances the degradation of nonsense-mediated decay substrates

Project description:Nonsense-mediated mRNA decay (NMD) controls gene expression by eliminating mRNAs with premature or aberrant translation termination. Degradation of NMD substrates is initiated by the central NMD factor UPF1, which recruits the endonuclease SMG6 and the deadenylation-promoting SMG5/7 complex. Here we map transcriptome-wide sites of SMG6-mediated endocleavage via 3′ fragment capture and degradome sequencing.

2017-06-01 | E-MTAB-3625 | biostudies-arrayexpress

Genome-wide analysis of Human Upf1, SMG5, SMG7 and PNRC2 downregulated substrates in HeLa cell

2012-11-01 | GSE34876 | GEO

TDRD6 instructs correct assembly of mRNPs in the chromatoid body to potentiate UPF1 dependent mRNA decay.

Project description:RNA sequencing of heterozygote or Tudor domain contian protein 6 (TDRD6) knockout round spermatid cells. Chromatoid bodies (CBs) are germ cell-specific organelles of largely unknown function. CBs harbor various RNA species, RNA-associated proteins and proteins of the tudor domain family such as TDRD6. Proteome analysis of purified CBs revealed components of the nonsense-mediated mRNA decay machinery such as UPF1. TDRD6 is essential for UPF1 localization to CBs, for UPF1-UPF2 interaction, and for assembly of UPFs and other RNA binding proteins into super-complexes. In absence of TDRD6, the association of some mRNAs with UPF1 is impaired, and the long 3’ UTR-stimulated but not the exon junction complex-stimulated pathway of NMD is distorted. Reduced association of mRNAs with UPF1 correlated with increased stability and presence in polysome fractions, i.e. enhanced translational activity. Thus, we define CBs as sites of UPF1-dependent mRNA degradation and provide evidence for the requirement for NMD in spermiogenesis. This function of CBs depends on TDRD6-promoted assembly of mRNA decay enzymes within mRNPs.

2015-12-08 | GSE63948 | GEO

Genome-wide analysis of Human Upf1, SMG5, SMG7 and PNRC2 downregulated substrates in HeLa cell

Project description:Analysis of cellular NMD (Nonsense-mediated mRNA decay) substrates that regulated by Upf1, SMG5, SMG7 and/or PNRC2 in HeLa cell. The hypothesis tested in the present study was that endogenous NMD substrates may co-regulated by Upf1, SMG5, SMG7 and PNRC2. Total RNA obtained from HeLa cells with downregulation of Upf1, SMG5, PNRC2 or SMG7 by siRNA. The up- or down-regulated transcripts were compare to control siRNA treated HeLa cell RNA extract. Significant transcripts were confirmed by replication

2012-11-01 | E-GEOD-34876 | biostudies-arrayexpress

UPF1 helicase orchestrates mutually exclusive interactions with the SMG6 endonuclease and UPF2

Project description:Nonsense-mediated mRNA decay (NMD) is a conserved co-translational mRNA surveillance and turnover pathway across eukaryotes. NMD has a central role in degrading defective mRNAs and also regulates the stability of a significant portion of the transcriptome. The pathway is organized around UPF1, an RNA helicase that can interact with several NMD-specific factors. In human cells, degradation of the targeted mRNAs begins with a cleavage event that requires the recruitment of the SMG6 endonuclease to UPF1. Previous studies have identified functional links between SMG6 and UPF1, but the underlying molecular mechanisms have remained elusive. In this work, we used mass spectrometry, structural biology and biochemical approaches to identify and characterize a conserved short linear motif in SMG6 that interacts with the cysteine/histidine-rich (CH) domain of UPF1. Unexpectedly, we found that the UPF1-SMG6 interaction is precluded when the UPF1 CH domain is engaged with another NMD factor, UPF2. Based on cryo-EM data, we propose that the formation of distinct SMG6-containing and UPF2-containing NMD complexes may be dictated by the RNA-binding status of UPF1. Our findings rationalize a key event in the metazoan NMD quality control pathway and progress our understanding of mechanisms regulating activity and guiding substrate recognition by the SMG6 endonuclease.

2024-05-01 | PXD049474 | Pride

Genome-wide analysis of cellular SMD or NMD substrates that regulated by Upf1 or PNRC2 in HeLa cell

Project description:Analysis of cellular SMD or NMD substrates that regulated by Upf1 and/or PNRC2 in HeLa cell. The hypothesis tested in the present study was that endogenous SMD or NMD substrates may co-regulated by Upf1 and PNRC2. Results provide important information that vast range of cellular SMD or NMD substrates are reqired PNRC2 for decay.

2012-02-28 | GSE26781 | GEO

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