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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 01, 2024 |
| Title |
Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition (csRNA-seq) |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has remained in question. Combining csRNA-seq, ATAC-seq and smFISH in Arabidopsis thaliana we demonstrate that active transcription initiation is detectable during the entire germination process. Features of non-coding regulation such as dynamic changes in chromatin accessible regions, antisense transcription, as well as bidirectional non-coding promoters are widespread throughout the Arabidopsis genome. We show that sensitivity to exogenous ABSCISIC ACID (ABA) during germination depends on proximal promoter accessibility at ABA-responsive genes. Moreover, we provide genetic validation of the existence of divergent transcription in plants. Our results reveal that active enhancer elements are transcribed producing non-coding enhancer RNAs (eRNAs) as widely documented in metazoans. In sum, this study defining the extent and role of coding and non-coding transcription during key stages of germination expands our understanding of transcriptional mechanisms underlying plant developmental transitions.
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| Overall design |
Capped-small RNA sequencing (csRNA-seq) from seeds and early germinating Arabidopsis thaliana plants.
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| Contributor(s) |
Tremblay BJ, Santini CP, Cheng Y, Zhang X, Rosa S, Qüesta JI |
| Citation(s) |
38409232 |
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| Submission date |
Dec 15, 2023 |
| Last update date |
Feb 27, 2024 |
| Contact name |
Julia I. Qüesta |
| E-mail(s) |
julia.questa@cragenomica.es
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| Organization name |
Centre for Research in Agricultural Genomics
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| Street address |
Carrer de la Vall Moronta
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| City |
Cerdanyola del Vallès |
| State/province |
Barcelona |
| ZIP/Postal code |
08193 |
| Country |
Spain |
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| Platforms (1) |
| GPL19580 |
Illumina NextSeq 500 (Arabidopsis thaliana) |
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| Samples (32)
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| GSM7977699 |
Germinating seed, 24h stratification, rep2, csRNA-seq |
| GSM7977700 |
Germinating seed, 72h stratification, rep1, csRNA-seq |
| GSM7977701 |
Germinating seed, 72h stratification, rep2, csRNA-seq |
| GSM7977702 |
Germinating seed, 6h light, rep1, csRNA-seq |
| GSM7977703 |
Germinating seed, 6h light, rep2, csRNA-seq |
| GSM7977704 |
Germinating seed, 26h light, rep1, csRNA-seq |
| GSM7977705 |
Germinating seed, 26h light, rep2, csRNA-seq |
| GSM7977706 |
Seedling, 57h light, rep1, csRNA-seq |
| GSM7977707 |
Seedling, 57h light, rep2, csRNA-seq |
| GSM7977708 |
hen2-4, 57h light, rep1, csRNA-seq |
| GSM7977709 |
hen2-4, 57h light, rep2, csRNA-seq |
| GSM7977710 |
rrp4-2, 57h light, rep1, csRNA-seq |
| GSM7977711 |
rrp4-2, 57h light, rep2, csRNA-seq |
| GSM7977712 |
Dry seed, rep1, sRNA-seq |
| GSM7977713 |
Dry seed, rep2, sRNA-seq |
| GSM7977714 |
Germinating seed, 24h stratification, rep1, sRNA-seq |
| GSM7977715 |
Germinating seed, 24h stratification, rep2, sRNA-seq |
| GSM7977716 |
Germinating seed, 72h stratification, rep1, sRNA-seq |
| GSM7977717 |
Germinating seed, 72h stratification, rep2, sRNA-seq |
| GSM7977718 |
Germinating seed, 6h light, rep1, sRNA-seq |
| GSM7977719 |
Germinating seed, 6h light, rep2, sRNA-seq |
| GSM7977720 |
Germinating seed, 26h light, rep1, sRNA-seq |
| GSM7977721 |
Germinating seed, 26h light, rep2, sRNA-seq |
| GSM7977722 |
Seedling, 57h light, rep1, sRNA-seq |
| GSM7977723 |
Seedling, 57h light, rep2, sRNA-seq |
| GSM7977724 |
hen2-4, 57h light, rep1, sRNA-seq |
| GSM7977725 |
hen2-4, 57h light, rep2, sRNA-seq |
| GSM7977726 |
rrp4-2, 57h light, rep1, sRNA-seq |
| GSM7977727 |
rrp4-2, 57h light, rep2, sRNA-seq |
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| This SubSeries is part of SuperSeries: |
| GSE250331 |
Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition. |
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| Relations |
| BioProject |
PRJNA1053374 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE250329_RAW.tar |
77.9 Mb |
(http)(custom) |
TAR (of BEDGRAPH, BW) |
| GSE250329_counts.cpm.csRNAseq.tsv.gz |
2.0 Mb |
(ftp)(http) |
TSV |
| GSE250329_counts.raw.csRNAseq.tsv.gz |
641.5 Kb |
(ftp)(http) |
TSV |
| GSE250329_tss.csRNAseq.bed.gz |
477.9 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
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