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| Status |
Public on Jun 04, 2024 |
| Title |
Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in Arabidopsis |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Transcription of antisense long noncoding RNAs (lncRNAs) occurs pervasively across eukaryotic genomes. Only a few antisense lncRNAs have been characterized and shown to control biological processes, albeit with idiosyncratic regulatory mechanisms. Thus, we largely lack knowledge about the general role of antisense transcription in eukaryotic organisms. Here, we characterized genes with antisense transcription initiating close to the Poly(A) signal (PAS genes) in Arabidopsis (Arabidopsis thaliana). We compared plant native elongation transcript sequencing (plaNET-seq) with RNA sequencing (RNA-seq) during short-term cold exposure and detected massive differences between the response in active transcription and steady-state levels of PAS gene-derived mRNAs. The cold-induced expression of transcription factors B-BOX DOMAIN PROTEIN28 (BBX28) and C2H2-TYPE ZINC FINGER FAMILY PROTEIN5 (ZAT5) was detected by plaNET-seq, while their steady-state level was only slightly altered due to high mRNA turnover. Knockdown of BBX28 and ZAT5 or of their respective antisense transcripts severely compromised plant freezing tolerance. Decreased antisense transcript expression levels resulted in a reduced cold response of BBX28 and ZAT5, revealing a positive regulatory role of both antisense transcripts. This study expands the known repertoire of noncoding transcripts. It highlights that native transcription approaches can complement steady state RNA techniques to identify biologically relevant players in stress responses.
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| Overall design |
WT (Col-0) Arabidopsis seedlings (12 day old) were subjected to cold (4°C) for 12h after which RNA was isolated and sent for sequencing.
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| Web link |
https://doi.org/10.1093/plcell/koae160
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| Contributor(s) |
Peter K, Susheel Sagar B |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jan 09, 2024 |
| Last update date |
Jun 05, 2024 |
| Contact name |
Peter Kindgren |
| E-mail(s) |
peter.kindgren@slu.se
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| Organization name |
Swedish University of Agricultural Sciences
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| Department |
Department of Forest Genetics and Plant Physiology
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| Street address |
KB5C5, KBC building, Linnaeus väg 6
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| City |
Umea |
| State/province |
Vasterbotten |
| ZIP/Postal code |
90736 |
| Country |
Sweden |
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| Platforms (1) |
| GPL26208 |
Illumina NovaSeq 6000 (Arabidopsis thaliana) |
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| Samples (9)
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| GSM8008701 |
Col-0, control (22°C), 0h, Bio Replicate 1 |
| GSM8008702 |
Col-0, control (22°C), 0h, Bio Replicate 2 |
| GSM8008703 |
Col-0, control (22°C), 0h, Bio Replicate 3 |
| GSM8008704 |
Col-0, cold (4°C), 3h, Bio Replicate 1 |
| GSM8008705 |
Col-0, cold (4°C), 3h, Bio Replicate 2 |
| GSM8008706 |
Col-0, cold (4°C), 3h, Bio Replicate 3 |
| GSM8008707 |
Col-0, cold (4°C), 12h, Bio Replicate 1 |
| GSM8008708 |
Col-0, cold (4°C), 12h, Bio Replicate 2 |
| GSM8008709 |
Col-0, cold (4°C), 12h, Bio Replicate 3 |
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| Relations |
| BioProject |
PRJNA1062790 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE252832_RAW.tar |
6.6 Mb |
(http)(custom) |
TAR (of SF) |
SRA Run Selector |
| Raw data are available in SRA |
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