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Series GSE129523 Query DataSets for GSE129523
Status Public on Oct 29, 2019
Title Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary RNA polymerase II (RNAPII) transcription converts the DNA sequence of a single gene into multiple transcript isoforms that may carry alternative functions. Gene isoforms result from variable transcription start sites (TSSs) at the beginning and polyadenylation sites (PASs) at the end of transcripts. How alternative TSSs relate to variable PASs is poorly understood. Here, we identify both ends of RNA molecules in Arabidopsis thaliana by transcription isoform sequencing (TIF-seq) and report four transcript isoforms per expressed gene. While intragenic initiation represents a large source of regulated isoform diversity, we observe that ~14% of expressed genes generate relatively unstable short promoter-proximal RNAs (sppRNAs) from nascent transcript cleavage and polyadenylation shortly after initiation. The location of sppRNAs correlates with the position of promoter-proximal RNAPII stalling, indicating that large pools of promoter-stalled RNAPII may engage in transcriptional termination. We propose that promoter-proximal RNAPII stalling-linked to premature transcriptional termination may represent a checkpoint that governs plant gene expression.
Overall design TIF-Seq was used to simultaneously map the transcription initiation sites and termination sites on A.thaliana seedlings (Col-0,Col-0 cold treated, HEN2-deficient genotype, HEN2-deficient cold treated and FACT-deficient genotypes). We also used TSS-Seq in these genotypes to validate the TIF-Seq analaysis and quantify initiation of transcription
Contributor(s) Thomas Q, Ard R, Liu J, Li B, Wang J, Pelechano V, Marquardt S
Citation(s) 32444691, 34058980
Submission date Apr 09, 2019
Last update date Jun 09, 2021
Contact name Quentin Angelo Pierre Thomas
Organization name University of Copenhagen
Department Dept. of Plant and Environmental Sciences
Street address Thorvaldsensvej 40
City Frederiksberg C
ZIP/Postal code 1871
Country Denmark
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (18)
GSM3714846 TIF-Seq in WT - rep 1
GSM3714847 TIF-Seq in WT - rep 2
GSM3714848 TIF-Seq in hen2-2 - rep 1
BioProject PRJNA531657
SRA SRP191544

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE129523_RAW.tar 14.5 Mb (http)(custom) TAR (of BEDGRAPH)
GSE129523_col-0.bed.gz 334.2 Kb (ftp)(http) BED
GSE129523_col-0cold.bed.gz 308.2 Kb (ftp)(http) BED
GSE129523_hen2-2.bed.gz 354.3 Kb (ftp)(http) BED
GSE129523_hen2-2cold.bed.gz 237.2 Kb (ftp)(http) BED
GSE129523_spt16-1.bed.gz 362.4 Kb (ftp)(http) BED
GSE129523_ssrp1-2.bed.gz 301.9 Kb (ftp)(http) BED
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Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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