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Homo sapiens

ABSTRACT: Human Nonsense-Mediated RNA Decay Initiates Widely by Endonucleolysis and Targets snoRNA Host Genes

PROVIDER: PRJNA246451 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1275420.fastq.gz	Fastqsanger.gz
	SRR1275421.fastq.gz	Fastqsanger.gz
	SRR1275413_1.fastq.gz	Fastqsanger.gz
	SRR1275413_2.fastq.gz	Fastqsanger.gz
	SRR1275414_1.fastq.gz	Fastqsanger.gz

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Human Nonsense-Mediated RNA Decay Initiates Widely by Endonucleolysis and Targets snoRNA Host Genes

Project description:Eukaryotic RNAs with premature termination codons (PTCs) are eliminated by nonsense-mediated decay (NMD). While human nonsense RNA degradation can be initiated either by an endonucleolytic cleavage event near the PTC or through decapping, the individual contribution of these activities on endogenous substrates has remained unresolved. Here we unambiguously establish that SMG6-catalyzed endonucleolysis is the primary initiating step in human nonsense RNA decay. We also show that both protein-coding and ‘non-coding’ genes hosting snoRNAs in their introns produce considerable amounts of NMD-sensitive splice variants, suggesting that these RNAs are merely by-products of a primary snoRNA production process. Finally, genes encoding multiple snoRNAs generally yield elevated numbers of alternative transcript isoforms, enabling the differential expression of individual snoRNAs. These findings demonstrate a hitherto unappreciated potential for decoupling of the individual expression levels of functional exon- and intron-encoded species from such composite genes. HEK293 Flp-In T-Rex cells were subjected to siRNA-mediated depletion of XRN1 and co-depletion of XRN1 with either SMG6 or UPF1. All the treated samples together with the controls were subjected to both RNA-seq and 5'-end-seq. RNA-seq was used for detecting NMD isoforms and their expression levels. 5'-end-seq was used for finding NMD decay intermediates (decapped and endocleaved molecules). CAGE was used to distinguish decapped from endocleaved RNA fragments.

2014-11-18 | E-GEOD-57433 | biostudies-arrayexpress

Human Nonsense-Mediated RNA Decay Initiates Widely by Endonucleolysis and Targets snoRNA Host Genes

Project description:Eukaryotic RNAs with premature termination codons (PTCs) are eliminated by nonsense-mediated decay (NMD). While human nonsense RNA degradation can be initiated either by an endonucleolytic cleavage event near the PTC or through decapping, the individual contribution of these activities on endogenous substrates has remained unresolved. Here we unambiguously establish that SMG6-catalyzed endonucleolysis is the primary initiating step in human nonsense RNA decay. We also show that both protein-coding and ‘non-coding’ genes hosting snoRNAs in their introns produce considerable amounts of NMD-sensitive splice variants, suggesting that these RNAs are merely by-products of a primary snoRNA production process. Finally, genes encoding multiple snoRNAs generally yield elevated numbers of alternative transcript isoforms, enabling the differential expression of individual snoRNAs. These findings demonstrate a hitherto unappreciated potential for decoupling of the individual expression levels of functional exon- and intron-encoded species from such composite genes. ------------------------------------------------------------------------------------- This article was corrected in http://genesdev.cshlp.org/content/30/9/1128.short Completely mapped 5'p-end sequencing data from the corrigendum have been updated in corresponding samples.

2014-11-18 | GSE57433 | GEO

Search for recessive retinitis pigmentosa genes using RNA expression analysis in lymphoblasts

Project description:Recessive retinitis pigmentosa (RP) is often caused by nonsense mutations that lead to low mRNA levels as a result of nonsense-mediated decay. Some RP genes are expressed at detectable levels in leukocytes as well as in the retina. We designed a microarray-based method to find recessive RP genes based on low lymphoblast mRNA expression levels Keywords: Recessive mutations; mRNA expression; nonsense mediated-decay; retinitis pigmentosa; lymphocyte; Affymetrix genechip Human Genome U133Plus2.0.

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3' UTR length and mRNP composition determine endocleavage efficiencies at termination codons

Project description:We aimed to study the cleavage sites of nonsense-mediated mRNA decay (NMD) substrates. Therefore, we depleted the major exoribonuclease XRN1 in human cell culture, which degrades the 3' fragments generated by SMG6-mediated endonucleolytic cleavage. Different reporter mRNAs or endogenous NMD targets were investigated and the 3' fragments were cloned, amplified and subsequently subjected to high throughput sequencing.

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Canonical poly(A) polymerase activity promotes the decay of a wide variety of mammalian nuclear RNAs

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