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Series GSE250330 Query DataSets for GSE250330
Status Public on Feb 01, 2024
Title Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition (ATAC-seq)
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
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.
 
Overall design Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) from seeds and early germinating Arabidopsis thaliana plants.
 
Contributor(s) Tremblay BJ, Santini CP, Cheng Y, Zhang X, Rosa S, Qüesta JI
Citation(s) 38409232
Submission date Dec 15, 2023
Last update date Feb 27, 2024
Contact name Julia I. Qüesta
E-mail(s) julia.questa@cragenomica.es
Organization name Centre for Research in Agricultural Genomics
Street address Carrer de la Vall Moronta
City Cerdanyola del Vallès
State/province Barcelona
ZIP/Postal code 08193
Country Spain
 
Platforms (1)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
Samples (8)
GSM7977728 Dry seed, rep1, ATAC-seq
GSM7977729 Dry seed, rep2, ATAC-seq
GSM7977730 Germinating seed, 6h light, rep1, ATAC-seq
This SubSeries is part of SuperSeries:
GSE250331 Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition.
Relations
BioProject PRJNA1053373

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE250330_RAW.tar 328.2 Mb (http)(custom) TAR (of BW)
GSE250330_counts.cpm.ATACseq.tsv.gz 2.0 Mb (ftp)(http) TSV
GSE250330_counts.raw.ATACseq.tsv.gz 442.4 Kb (ftp)(http) TSV
GSE250330_peaks.ATACseq.bed.gz 502.8 Kb (ftp)(http) BED
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Raw data are available in SRA

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