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HnRNP L protects mRNAs from nonsense-mediated mRNA decay

ABSTRACT: hnRNP L protects mRNAs from nonsense-mediated mRNA decay

PROVIDER: PRJNA429768 | ENA |

REPOSITORIES: ENA

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hnRNP L protects mRNAs from nonsense-mediated mRNA decay

Project description:Identification of RNAs differentially expressed upon treatment with nontargeting siRNA, hnRNP L siRNA, UPF1 siRNA, or hnRNP L and UPF1 siRNAs together.

2018-12-05 | GSE109143 | GEO

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Activation of nonsense-mediated mRNA decay protects against C9orf72 dipeptide-repeat neurotoxicity

Project description:Activation of nonsense-mediated mRNA decay protects against C9orf72 dipeptide-repeat neurotoxicity

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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

Ultraconserved elements are associated with control of splicing regulators by alt splicing and nonsense mediated decay

Project description:We blocked nonsense-mediated mRNA decay (NMD) pathway and used a custom alternative transcript sensitive Affymetrix microarray to seek alternatively spliced RNAs whose levels increased compared to controls. Keywords: Nonsense Mediated Decay (NMD)

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RNAi knock down of known nonsense-mediated mRNA decay (NMD) factors in Drosophila cells

Project description:All eukaryotes studied to date have the capacity to detect and degrade mRNAs harboring premature translation termination codons (PTCs) in a process called nonsense-mediated mRNA decay (NMD) (reviewed in Wagner E & Lykke-Andersen J, 2002). This surveillance system allows the cell to prevent the expression of potentially harmful truncated proteins. trans-acting factors required for NMD in Drosophila are the proteins UPF1, UPF2, UPF3, SMG-1, SMG-5 and SMG-6. To identify mRNAs naturally regulated by NMD, we analyzed expression profiles in Drosophila cells RNAi-depleted of known NMD factors using high-density oligonucleotide arrays.

2005-11-01 | E-MEXP-202 | biostudies-arrayexpress

Analysis of nonsense-mediated mRNA decay in daf-2 mutants

Project description:To exmine the role of nonsense-mediated mRNA decay process in the longevity regulation of daf-2 mutants, we sequenced transcriptomes from day 1 adult Caenorhabditis elegans: Bristol N2 (wild-type), and smg-2(qd101), daf-2(e1370) and smg-2(qd101); daf-2(e1370) mutants.

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Target discrimination in nonsense-mediated mRNA decay requires Upf1 ATPase activity (CLIP-Seq)

Project description:RNA quality control pathways serve to get rid of faulty RNAs and therefore must be able to discriminate these RNAs from those that are normal. Here we present evidence that the ATPase cycle of SF1 Helicase Upf1 is required for mRNA discrimination during Nonsense-Mediated Decay (NMD). Mutations affecting the Upf1 ATPase cycle disrupt the mRNA selectivity of Upf1, leading to indiscriminate accumulation of NMD complexes on both NMD target and non-target mRNAs. In addition, two modulators of NMD - translation and termination codon-proximal poly(A) binding protein - depend on Upf1 ATPase to limit Upf1-non-target association. Preferential ATPase-dependent dissociation of Upf1 from non-target mRNAs in vitro suggests that selective release of Upf1 contributes to the ATPase-dependence of Upf1 target discrimination. Given the prevalence of helicases in RNA regulation, ATP hydrolysis may be an underappreciated, yet widely employed, activity in target RNA discrimination. CLIP and RIP-seq against Wild Type and Mutant Upf1 in HEK293-T cell lines

2015-07-06 | E-GEOD-69584 | biostudies-arrayexpress

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2015-07-06 | E-GEOD-69585 | biostudies-arrayexpress

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