Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay enzymes

Axel Thieffry, Jette Bornholdt, Maxim Ivanov, Peter Brodersen, Albin Sandelin
doi: https://doi.org/10.1101/809194
Axel Thieffry
1Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
2Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jette Bornholdt
1Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
2Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Maxim Ivanov
3Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Peter Brodersen
1Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: pbrodersen@bio.ku.dk albin@binf.ku.dk
Albin Sandelin
1Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
2Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: pbrodersen@bio.ku.dk albin@binf.ku.dk
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

ABSTRACT

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. Similarly, active enhancer regions in animals initiate transcription of exosome-sensitive enhancer RNAs (eRNAs). 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 and eRNAs in A. thaliana. While PROMPTs are overall rare in A. thaliana, about 100 clear cases of exosome-sensitive PROMPTs and 113 loci producing eRNA-like transcripts were identified. In addition, we found ∼200 transcription start sites within 3’-UTR-encoding regions that produce unspliced exosome-sensitive antisense RNAs covering much of the cognate pre-mRNA. A typical representative of this class of RNAs is the previously characterized non-coding RNA controlling the expression of the key seed dormancy regulator, DELAY OF GERMINATION1. Exosome-sensitive antisense RNAs are overrepresented in transcription factor genes, suggesting a potential for widespread control of gene expression. Lastly, we assess the use of alternative promoters in A. thaliana and compare the accuracy of existing TSS annotations.

Footnotes

  • We found an alignment 1 bp indexing error on minus strand for nanoPARE TSS data (Thanks to Michael Schon for making us aware of the issue), which is used for comparison with CAGE data in Figure 3. This is now corrected. This changes changes the nanoPARE logo in Figure 3C and very subtle the nanoPARE profile plots in Figure 3. Small text changes are made to comment on the change. This does not change any major conclusions in the paper.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted October 23, 2019.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay enzymes
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay enzymes
Axel Thieffry, Jette Bornholdt, Maxim Ivanov, Peter Brodersen, Albin Sandelin
bioRxiv 809194; doi: https://doi.org/10.1101/809194
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay enzymes
Axel Thieffry, Jette Bornholdt, Maxim Ivanov, Peter Brodersen, Albin Sandelin
bioRxiv 809194; doi: https://doi.org/10.1101/809194

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4235)
  • Biochemistry (9136)
  • Bioengineering (6784)
  • Bioinformatics (24001)
  • Biophysics (12129)
  • Cancer Biology (9534)
  • Cell Biology (13778)
  • Clinical Trials (138)
  • Developmental Biology (7636)
  • Ecology (11702)
  • Epidemiology (2066)
  • Evolutionary Biology (15513)
  • Genetics (10644)
  • Genomics (14326)
  • Immunology (9483)
  • Microbiology (22839)
  • Molecular Biology (9090)
  • Neuroscience (48995)
  • Paleontology (355)
  • Pathology (1482)
  • Pharmacology and Toxicology (2570)
  • Physiology (3846)
  • Plant Biology (8331)
  • Scientific Communication and Education (1471)
  • Synthetic Biology (2296)
  • Systems Biology (6192)
  • Zoology (1301)