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| Status |
Public on Feb 01, 2023 |
| Title |
Promoter-pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Eukaryotic genomes are pervasively transcribed by RNA polymerase II. Yet, the molecular and biological implications of such a phenomenon are still largely puzzling. Here, we describe noncoding RNA transcription upstream of the Arabidopsis thaliana DOG1 gene, which governs salt stress responses and is a key regulator of seed dormancy. We find that expression of the DOG1 gene is induced by salt stress, thereby causing a delay in seed germination. We uncover extensive transcriptional activity on the promoter of the DOG1 gene, which produces a variety of lncRNAs. These lncRNAs, named PUPPIES, are co-directionally transcribed and extend into the DOG1 coding region. We show that PUPPIES RNAs respond to salt stress and boost DOG1 expression, resulting in delayed germination. This positive role of pervasive PUPPIES transcription on DOG1 gene expression is associated with augmented pausing of RNA polymerase II, slower transcription and higher transcriptional burst size. These findings highlight the positive role of upstream co-directional transcription in controlling transcriptional dynamics of downstream genes.
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| Overall design |
Comparison of transcriptomes of Col-0 and dog1-3 (SALK_000867) mutant upon seed imbibition - control and salt stress conditions (four biological replicas).
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| Contributor(s) |
Montez M, Krzyszton M, Swiezewski S |
| Citation(s) |
36705062 |
| Submission date |
Jul 21, 2022 |
| Last update date |
Feb 03, 2023 |
| Contact name |
Michal Krzyszton |
| Organization name |
Institute of Biochemistry and Biophysics, Polish Academy of Sciences
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| Lab |
Laboratory of Seeds Molecular Biology
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| Street address |
Pawinskiego 5a
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| City |
Warsaw |
| ZIP/Postal code |
02-106 |
| Country |
Poland |
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| Platforms (1) |
| GPL26208 |
Illumina NovaSeq 6000 (Arabidopsis thaliana) |
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| Samples (16)
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| GSM6368930 |
Col0, control, 4 |
| GSM6368931 |
dog1, control, 1 |
| GSM6368932 |
dog1, control, 2 |
| GSM6368933 |
dog1, control, 3 |
| GSM6368934 |
dog1, control, 4 |
| GSM6368935 |
Col0, NaCl, 1 |
| GSM6368936 |
Col0, NaCl, 2 |
| GSM6368937 |
Col0, NaCl, 3 |
| GSM6368938 |
Col0, NaCl, 4 |
| GSM6368939 |
dog1, NaCl, 1 |
| GSM6368940 |
dog1, NaCl, 2 |
| GSM6368941 |
dog1, NaCl, 3 |
| GSM6368942 |
dog1, NaCl, 4 |
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| Relations |
| BioProject |
PRJNA860957 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE208755_RAW.tar |
1.9 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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