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Series GSE142555 Query DataSets for GSE142555
Status Public on Feb 17, 2020
Title Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay pathways
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary In animals, transcription by RNA polymerase II initiates bidirectionally from gene promoters to produce pre-mRNAs on the forward strand and promoter upstream transcripts (PROMPTs) on the reverse strand. PROMPTs are rapidly degraded by the nuclear exosome. Previous studies based on nascent RNA approaches concluded that Arabidopsis thaliana does not produce PROMPTs. Here, we used steady-state RNA sequencing methods in mutants defective in nuclear RNA decay, including by the exosome, to reassess the existence of PROMPTs in A. thaliana. While PROMPTs are overall rare in A. thaliana, about 100 clear cases of exosome-sensitive PROMPTs were identified. We also found that PROMPTs become sources of 21-22 nt small interfering RNAs in exosome-deficient mutants, perhaps explaining why plants have evolved mechanisms to suppress PROMPT production. In addition, we found ~200 transcription start sites within 3’-UTR-encoding regions that produce long unspliced, exosome-sensitive antisense RNAs. The previously characterized non-coding (nc) RNA that regulates expression of the key seed dormancy regulator, DELAY OF GERMINATION1, is a typical representative of this class of RNAs. Transcription factor genes are overrepresented among loci with exosome-sensitive antisense RNAs, suggesting a potential for widespread control of gene expression via this class of ncRNAs. Lastly, we assess the use of alternative promoters in A. thaliana and compare the accuracy of existing TSS annotations.
Overall design small RNA-seq sequencing of leaf and young flower bud tissues in wt, hen2-5 and rrp4-2 mutants
Contributor(s) Thieffry A, Vigh M, Bornholdt J, Ivanov M, Brodersen P, Sandelin A
Citation(s) 32213639
Submission date Dec 23, 2019
Last update date Mar 30, 2020
Contact name Axel Thieffry
Organization name BioPhero-FMC
Department R&D
Street address Lersø Parkallé 42-44
City Copenhagen
State/province Hovedstaden
ZIP/Postal code 2100
Country Denmark
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (12)
GSM4231872 flower.hen2-5_R1
GSM4231873 flower.hen2-5_R2
GSM4231874 flower.rrp4-2_R1
BioProject PRJNA597366
SRA SRP238624

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Supplementary file Size Download File type/resource
GSE142555_RAW.tar 886.2 Mb (http)(custom) TAR (of BW)
GSE142555_sample_info.xlsx 10.3 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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