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E-MTAB-5132

ABSTRACT: Direct RNA Sequencing of polyadenylated RNA & high-depth Illumina strand-specific, short read RNA-seq of a stably RNAi-silenced nuclear 5'-3' exonuclease XRN3 mutant line in Arabidopsis thaliana

PROVIDER: E-MTAB-5132 | ExpressionAtlas | 2016-12-15

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-MTAB-5132-analysis-methods.tsv	Tabular
	E-MTAB-5132-analytics.tsv	Tabular
	E-MTAB-5132-atlasExperimentSummary.Rdata	Rdata
	E-MTAB-5132-configuration.xml	Xml
	E-MTAB-5132-g3_g4-mvaPlot.png	Other

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E-MTAB-5137

Project description:Transcription profiling by array of a stably RNAi-silenced nuclear 5-3 exonuclease XRN3 mutant line in Arabidopsis thaliana after transcriptional inhibition with cordycepin

2016-10-06 | E-MTAB-5137 | ExpressionAtlas

Direct RNA Sequencing of polyadenylated RNA & high-depth Illumina strand-specific, short read RNA-seq of a stably RNAi-silenced nuclear 5’-3’ exonuclease XRN3 mutant line in Arabidopsis thaliana

Project description:Direct RNA Sequencing of polyadenylated RNA & high-depth Illumina strand-specific, short read RNA-seq of a stably RNAi-silenced nuclear 5’-3’ exonuclease XRN3 mutant line in Arabidopsis thaliana

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Transcription profiling by array of a stably RNAi-silenced nuclear 5’-3’ exonuclease XRN3 mutant line in Arabidopsis thaliana after transcriptional inhibition with cordycepin

Project description:In Arabidopsis thaliana two nuclear 5'-3' exonucleases, XRN2 & 3, are involved in the degradation and processing of several classes of nuclear RNAs and in transcription termination of RNA polymerase II. The role of XRN3 in Pol II transcription termination is investigated by combining two different types of RNA-seq data for Col-0 background WT and xrn3-8 mutant A. thaliana seedlings. The data for the experiment comprises single molecule Direct RNA Sequencing of unamplified RNA (3x WT, 4x xrn3-8 mutant) and high-depth Illumina strand-specific short read sequencing of PCR amplified ribosomal-RNA depleted RNA (Illumina TruSeq stranded ribozero Plant kit, 3x WT, 3x xrm3-8 mutant). In the xrn3 mutant, these data reveal a widespread accumulation of non-coding intergenic transcripts (xrn3-associated transcripts - XATs) generated by Pol II read-through transcription that are usually polyadenylated and lack the 5' cap structure. This data highlights the important role of exoribonucleases in the torpedo mechanism of Pol II transcription termination and show that a global disturbance in this process significantly impacts both gene expression and transcriptome integrity.

2019-09-02 | E-MTAB-5137 | biostudies-arrayexpress

Direct RNA Sequencing of polyadenylated RNA & high-depth Illumina strand-specific, short read RNA-seq of a stably RNAi-silenced nuclear 5'-3' exonuclease XRN3 mutant line in Arabidopsis thaliana

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Defective XRN3-mediated transcription termination in Arabidopsis affects the expression of protein-coding genes [seq]

Project description:Arabidopsis thaliana contains two nuclear XRN2/3 5'-3' exonucleases that are homologs of yeast and human Rat1/Xrn2 proteins involved in the processing and degradation of several classes of nuclear RNAs and in transcription termination of RNA polymerase II. Using strand-specific short read sequencing we show that knockdown of XRN3 leads to an altered expression of hundreds of genes and the accumulation of uncapped and polyadenylated read-through transcripts generated by inefficiently terminated Pol II. Our data support the notion that XRN3-mediated changes in the expression of a subset of genes are caused by upstream read-through transcription and these effects are enhanced by RNA-mRNA chimeras generated in xrn3 plants. In turn, read-through transcripts that are antisense to downstream genes may trigger production of siRNA. Our results highlight the importance of XRN3 exoribonuclease in Pol II transcription termination in plants and show that disturbance in this process may significantly alter gene expression.

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