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

Matthew Parker, Katarzyna Knop, Vasiliki Zacharaki, Anya Sherwood, Daniel Tomé, Xuhong Yu, Pascal Martin, Jim Beynon, Scott Michaels, Geoffrey J. Barton, Gordon G. Simpson (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review

27 Citations (Scopus)
158 Downloads (Pure)


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.
Original languageEnglish
Article numbere65537
Number of pages36
Early online date27 Apr 2021
Publication statusPublished - 12 May 2021


  • NLR
  • Nanopore
  • direct RNA sequencing
  • spen
  • FPA
  • m6A
  • alternative polyadenylation
  • chimeric RNA
  • disease resistance
  • transcription termination

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Neuroscience(all)


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