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ICLIP analysis of RNA substrates of the archaeal exosome (RNA-Seq)

ABSTRACT: iCLIP analysis of RNA substrates of the archaeal exosome (RNA-Seq)

PROVIDER: PRJNA627448 | ENA |

REPOSITORIES: ENA

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iCLIP analysis of RNA substrates of the archaeal exosome (iCLIP)

Project description:In this study, an exoribonuclease was analyzed by iCLIP. The data documents the role of the archaeal exosome as an exoribonuclease and RNA-tailing enzyme interacting with all RNA classes. Mapping of most reads to mRNAs underlines the role of exosome in mRNA turnover, which is important for adaptation of prokaryotic cells to changing environmental conditions. The clustering of crosslink sites near 5’-ends of genes suggests simultaneous binding of both RNA ends by the S. solfataricus exosome. This may serve to prevent translation of mRNAs designated to degradation in 3’-5’ direction.

2020-11-24 | GSE149140 | GEO

iCLIP analysis of RNA substrates of the archaeal exosome (iCLIP)

Project description:iCLIP analysis of RNA substrates of the archaeal exosome (iCLIP)

| PRJNA627449 | ENA

iCLIP analysis of RNA substrates of the archaeal exosome (RNA-Seq)

2020-11-24 | GSE149142 | GEO

iCLIP analysis of RNA substrates of the archaeal exosome

Project description:iCLIP analysis of RNA substrates of the archaeal exosome

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iCLIP analysis of RNA substrates of the archaeal exosome.

Project description: Not available

| S-EPMC7667871 | biostudies-literature

iCLIP analysis of RNA substrates of the archaeal exosome

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-11-24 | GSE149143 | GEO

Analyses of endogenous rna substrates of xrn and exosome and ptgs pathways; Integrating RNA Quality Control and RNA Silencing Pathways

Project description:blan08_rnapaths; Analyses of endogenous rna substrates of xrn and exosome and ptgs pathways What are the endogenous RNA substrates co-regulated by RQC and PTGS pathways? Genome-wide analyses of endogenous RNA substrates of RNA Quality Control pathways; wild type versus 15 mutants. 30 dye-swap - gene knock in (transgenic), gene knock out

2013-06-26 | E-GEOD-48192 | biostudies-arrayexpress

Analyses of endogenous rna substrates of xrn and exosome and ptgs pathways; Integrating RNA Quality Control and RNA Silencing Pathways

2013-06-26 | GSE48192 | GEO

Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the Arabidopsis Transcriptome

Project description:The exosome complex plays a central role in RNA metabolism, and each of its core subunits is essential for viability in yeast However, comprehensive studies of exosome substrates and functional analyses of its subunits in multi.CELlular eukaryotes are lacking Here we show that, in sharp contrast to yeast and metazoan exosome complexes, individual subunits of the plant exosome core are functionally specialized Using whole-genome oligonucleotide tiling microarray analyses of csl4 null mutant plants and conditional genetic depletions of RRP4 and RRP41, we uncovered unexpected functional plasticity in the plant exosome core as well as generated a set of high-resolution genome-wide maps of Arabidopsis exosome targets These analyses provide evidence for widespread polyadenylation- and exosome-mediated RNA quality control in plants and reveal novel aspects of stable structural RNA metabolism Finally, numerous novel exosome substrates were discovered, including a select subset of mRNAs, miRNA processing intermediates, and hundreds of noncoding RNAs, the vast majority of which have not been previously described This large collection of RNAs belong to a Òdeeply hiddenÓ layer of the transcriptome that is tightly repressed and can only be visualized upon inhibition of exosome activity These first genome-wide maps of exosome substrates will aid in illuminating new fundamental components and regulatory mechanisms of eukaryotic transcriptomes Keywords: Strand-specific gene expression analysis using whole-genome oligonucleotide tiling microarray analyses of three exosome subunits, using csl4 null mutant plants and conditional genetic depletions of RRP4 and RRP41.

2007-12-28 | GSE9317 | GEO

Transcriptome-wide analysis of alternative routes for RNA substrates into the exosome complex

Project description:The RNA exosome complex functions in both the accurate processing and rapid degradation of many different classes of RNA. Functional and structural analyses indicate that RNA can either be threaded through the central channel of the exosome or more directly access the active sites of the ribonucleases Rrp44 and Rrp6, but it was unclear how many substrates follow each pathway in vivo. To address this we used UV crosslinking in growing cells to identify transcriptome-wide interactions of RNAs with the major nuclear exosome-cofactor Mtr4 and with individual exosome subunits (Rrp6, Csl4, Rrp41 and Rrp44) along the threaded RNA path. We performed comparative analyses on exosome complexes lacking the exonucleolytic activity of Rrp44, either carrying a mutation in the Rrp44 S1 RNA-binding domain, predicted to disfavor direct access to the Rrp44 exonuclease active site, or with multiple mutations in Rrp41, reported to block RNA passage through the central channel. Our analysis identified targets using preferentially channel-threading pathway such as mRNAs, 5S rRNA or scR1. Our results suggest as well that aborted tRNAs transcripts, released during transcription, would be rapidly degraded using this route. Alternatively, pre-tRNAs appears to access Rrp44 directly. Both routes seems to be involved for degradation or maturation of RNAPI transcripts. The Rrp41 mutations were found to block substrate passage to Rrp44 only for cytoplasmic mRNAs, apparently confirming the prediction of widening of the lumen in the nuclear, Rrp6-associated complex.

2017-03-20 | GSE90647 | GEO

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