1. Chromosomes and Gene Expression
  2. Plant Biology

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

  1. Matthew T Parker
  2. Katarzyna Knop
  3. Vasiliki Zacharaki
  4. Anna V Sherwood
  5. Daniel Tome
  6. Xuhong Yu
  7. Pascal GP Martin
  8. Jim Beynon
  9. Scott Michaels
  10. Geoffrey John Barton
  11. Gordon Grant Simpson  Is a corresponding author
  1. University of Dundee, United Kingdom
  2. University of Warwick, United Kingdom
  3. Indiana University, United States
https://doi.org/10.7554/eLife.65537
Share this article
Cite this article
  1. Matthew T Parker
  2. Katarzyna Knop
  3. Vasiliki Zacharaki
  4. Anna V Sherwood
  5. Daniel Tome
  6. Xuhong Yu
  7. Pascal GP Martin
  8. Jim Beynon
  9. Scott Michaels
  10. Geoffrey John Barton
  11. Gordon Grant Simpson
(2021)
Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA
eLife 10:e65537.
https://doi.org/10.7554/eLife.65537
  2. Download BibTeX
  3. Download .RIS

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 (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, thereby controlling their functional expression and impacting immunity. Using long-read Nanopore direct RNA sequencing, we resolved 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.

Data availability

IVI-MS data is available from the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD022684. FPA and Pol II ChIP-Seq data is available from ENA accession PRJNA449914. Col-0 nanopore DRS data is available from ENA accession PRJEB32782. fpa-8 and 35S::FPA:YFP nanopore DRS data is available from ENA accession PRJEB41451. hen2-2 nanopore DRS data is available from ENA accession PRJEB41381. Col-0, fpa-8 and 35S::FPA:YFP Helicos DRS data is available from Zenodo DOI 10.5281/zenodo.4309752 ahead of submission to ENA. Col-0, fpa-8 and 35S::FPA:YFP Illumina RNA-Seq data is available from ENA accession PRJEB41455.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Matthew T Parker

    School of Life Sciences, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0891-8495

  2. Katarzyna Knop

    School of Life Sciences, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2636-9450

  3. Vasiliki Zacharaki

    School of Life Sciences, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5543-2332

  4. Anna V Sherwood

    School of Life Sciences, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  5. Daniel Tome

    School of Life Sciences, University of Warwick, Coventry, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  6. Xuhong Yu

    Department of Biology, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. Pascal GP Martin

    Department of Biology, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4271-658X

  8. Jim Beynon

    School of Life Sciences, University of Warwick, Coventry, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  9. Scott Michaels

    Department of Biology, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.

  10. Geoffrey John Barton

    School of Life Sciences, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9014-5355

  11. Gordon Grant Simpson

    School of Life Sciences, University of Dundee, Dundee, United Kingdom
    For correspondence
    g.g.simpson@dundee.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6744-5889

Funding

Biotechnology and Biological Sciences Research Council (BB/M010066/1)

  • Geoffrey John Barton
  • Gordon Grant Simpson

Biotechnology and Biological Sciences Research Council (BB/J00247X/1)

  • Geoffrey John Barton
  • Gordon Grant Simpson

Biotechnology and Biological Sciences Research Council (BB/M004155/1)

  • Geoffrey John Barton
  • Gordon Grant Simpson

H2020 Marie Skłodowska-Curie Actions (799300)

  • Katarzyna Knop

Wellcome (097945/B/11/Z)

  • Geoffrey John Barton
  • Gordon Grant Simpson

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2021, Parker et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 3,595
    views
  • 548
    downloads
  • 44
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Matthew T Parker
  2. Katarzyna Knop
  3. Vasiliki Zacharaki
  4. Anna V Sherwood
  5. Daniel Tome
  6. Xuhong Yu
  7. Pascal GP Martin
  8. Jim Beynon
  9. Scott Michaels
  10. Geoffrey John Barton
  11. Gordon Grant Simpson
(2021)
Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA
eLife 10:e65537.
https://doi.org/10.7554/eLife.65537

Share this article

https://doi.org/10.7554/eLife.65537

Categories and tags

Research organism

Further reading

    1. Chromosomes and Gene Expression

    Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy

    Carmina Lichauco, Eric J Foss ... Antonio Bedalov
    Research Article

    The association between late replication timing and low transcription rates in eukaryotic heterochromatin is well known, yet the specific mechanisms underlying this link remain uncertain. In Saccharomyces cerevisiae, the histone deacetylase Sir2 is required for both transcriptional silencing and late replication at the repetitive ribosomal DNA (rDNA) arrays. We have previously reported that in the absence of SIR2, a de-repressed RNA PolII repositions MCM replicative helicases from their loading site at the ribosomal origin, where they abut well-positioned, high-occupancy nucleosomes, to an adjacent region with lower nucleosome occupancy. By developing a method that can distinguish activation of closely spaced MCM complexes, here we show that the displaced MCMs at rDNA origins have increased firing propensity compared to the nondisplaced MCMs. Furthermore, we found that both activation of the repositioned MCMs and low occupancy of the adjacent nucleosomes critically depend on the chromatin remodeling activity of FUN30. Our study elucidates the mechanism by which Sir2 delays replication timing, and it demonstrates, for the first time, that activation of a specific replication origin in vivo relies on the nucleosome context shaped by a single chromatin remodeler.

    1. Chromosomes and Gene Expression

    Cryogenic Electron Microscopy: MagIC beads for scarce macromolecules

    Carlos Moreno-Yruela, Beat Fierz
    Insight

    Specialized magnetic beads that bind target proteins to a cryogenic electron microscopy grid make it possible to study the structure of protein complexes from dilute samples.

    1. Chromosomes and Gene Expression
    2. Structural Biology and Molecular Biophysics

    Surprising features of nuclear receptor interaction networks revealed by live-cell single-molecule imaging

    Liza Dahal, Thomas GW Graham ... Xavier Darzacq
    Research Article

    Type II nuclear receptors (T2NRs) require heterodimerization with a common partner, the retinoid X receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and overexpression studies, binding of T2NRs to chromatin is proposed to be regulated by competition for a limiting pool of the core RXR subunit. However, this mechanism has not yet been tested for endogenous proteins in live cells. Using single-molecule tracking (SMT) and proximity-assisted photoactivation (PAPA), we monitored interactions between endogenously tagged RXR and retinoic acid receptor (RAR) in live cells. Unexpectedly, we find that higher expression of RAR, but not RXR, increases heterodimerization and chromatin binding in U2OS cells. This surprising finding indicates the limiting factor is not RXR but likely its cadre of obligate dimer binding partners. SMT and PAPA thus provide a direct way to probe which components are functionally limiting within a complex TF interaction network providing new insights into mechanisms of gene regulation in vivo with implications for drug development targeting nuclear receptors.