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Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA

View ORCID ProfileMatthew T. Parker, View ORCID ProfileKatarzyna Knop, View ORCID ProfileVasiliki Zacharaki, Anna V. Sherwood, Daniel Tome, View ORCID ProfileXuhong Yu, View ORCID ProfilePascal Martin, Jim Beynon, View ORCID ProfileScott Michaels, View ORCID ProfileGeoffrey J. Barton, View ORCID ProfileGordon G. Simpson
doi: https://doi.org/10.1101/2020.12.15.422694
Matthew T. Parker
1School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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Katarzyna Knop
1School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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  • ORCID record for Katarzyna Knop
Vasiliki Zacharaki
1School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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Anna V. Sherwood
1School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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Daniel Tome
2School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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Xuhong Yu
3Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Pascal Martin
3Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Jim Beynon
2School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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Scott Michaels
3Department of Biology, Indiana University, Bloomington, IN 47405, USA
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  • ORCID record for Scott Michaels
Geoffrey J. Barton
1School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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Gordon G. Simpson
1School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
4The James Hutton Institute, Invergowrie DD2 5DA, UK
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  • For correspondence: g.g.simpson@dundee.ac.uk
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Abstract

Genes involved in disease resistance are some of the fastest evolving and most diverse components of genomes. Large numbers of nucleotide-binding, leucine-rich repeat receptor (NLR) genes are found in plant genomes and are required for disease resistance. However, NLRs can trigger autoimmunity, disrupt beneficial microbiota or reduce fitness. It is therefore crucial to understand how NLRs are controlled. Here we show that the RNA-binding protein FPA mediates widespread premature cleavage and polyadenylation of NLR transcripts, controlling their functional expression and impacting immunity. Using long-read nanopore direct RNA sequencing we resolve the complexity of NLR transcript processing and gene annotation. Our results uncover a co-transcriptional layer of NLR control with implications for understanding the regulatory and evolutionary dynamics of NLRs in the immune responses of plants.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://www.ebi.ac.uk/pride/archive/projects/PXD022684

  • https://www.ebi.ac.uk/ena/browser/view/PRJEB41451

  • https://zenodo.org/record/4309752

  • https://www.ebi.ac.uk/ena/browser/view/PRJEB41455

  • https://www.ebi.ac.uk/ena/browser/view/PRJEB41381

  • https://www.ebi.ac.uk/ena/browser/view/PRJEB32782

  • https://www.ebi.ac.uk/ena/browser/view/PRJNA449914

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-NC 4.0 International license.
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Posted December 15, 2020.
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Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA
Matthew T. Parker, Katarzyna Knop, Vasiliki Zacharaki, Anna V. Sherwood, Daniel Tome, Xuhong Yu, Pascal Martin, Jim Beynon, Scott Michaels, Geoffrey J. Barton, Gordon G. Simpson
bioRxiv 2020.12.15.422694; doi: https://doi.org/10.1101/2020.12.15.422694
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Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA
Matthew T. Parker, Katarzyna Knop, Vasiliki Zacharaki, Anna V. Sherwood, Daniel Tome, Xuhong Yu, Pascal Martin, Jim Beynon, Scott Michaels, Geoffrey J. Barton, Gordon G. Simpson
bioRxiv 2020.12.15.422694; doi: https://doi.org/10.1101/2020.12.15.422694

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