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| Status |
Public on Jan 24, 2018 |
| Title |
Defective XRN3-mediated transcription termination in Arabidopsis affects the expression of protein-coding genes [seq] |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
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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| Overall design |
Transcriptome profiles of Col-0 and xrn3-8 mutant plants using RNA-seq (three biological replicates) and small RNA-seq (three biological replicates).
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| Contributor(s) |
Krzyszton M, Zakrzewska-Placzek M, Kwasnik A, Dojer N, Karlowski W, Kufel J |
| Citation(s) |
29356198, 30949693 |
| |
| Submission date |
Feb 28, 2017 |
| Last update date |
Aug 05, 2022 |
| Contact name |
Michal Krzyszton |
| Organization name |
Institute of Biochemistry and Biophysics, Polish Academy of Sciences
|
| Lab |
Laboratory of Seeds Molecular Biology
|
| Street address |
Pawinskiego 5a
|
| City |
Warsaw |
| ZIP/Postal code |
02-106 |
| Country |
Poland |
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| Platforms (2) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
| GPL21785 |
Illumina HiSeq 4000 (Arabidopsis thaliana) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA377231 |
| SRA |
SRP100824 |
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