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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.<\/jats:p>","DOI":"10.7554\/elife.65537","type":"journal-article","created":{"date-parts":[[2021,4,27]],"date-time":"2021-04-27T09:37:12Z","timestamp":1619516232000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.65537","source":"Crossref","is-referenced-by-count":63,"title":["Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA"],"prefix":"10.7554","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0891-8495","authenticated-orcid":true,"given":"Matthew T","family":"Parker","sequence":"first","affiliation":[{"name":"School of Life Sciences, University of Dundee, Dundee, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2636-9450","authenticated-orcid":true,"given":"Katarzyna","family":"Knop","sequence":"additional","affiliation":[{"name":"School of Life Sciences, University of Dundee, Dundee, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5543-2332","authenticated-orcid":true,"given":"Vasiliki","family":"Zacharaki","sequence":"additional","affiliation":[{"name":"School of Life Sciences, University of Dundee, Dundee, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna V","family":"Sherwood","sequence":"additional","affiliation":[{"name":"School of Life Sciences, University of Dundee, Dundee, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Tom\u00e9","sequence":"additional","affiliation":[{"name":"School of Life Sciences, University of Warwick, Coventry, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuhong","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Biology, Indiana University, Bloomington, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4271-658X","authenticated-orcid":true,"given":"Pascal GP","family":"Martin","sequence":"additional","affiliation":[{"name":"Department of Biology, Indiana University, Bloomington, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jim","family":"Beynon","sequence":"additional","affiliation":[{"name":"School of Life Sciences, University of Warwick, Coventry, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5248-3487","authenticated-orcid":true,"given":"Scott D","family":"Michaels","sequence":"additional","affiliation":[{"name":"Department of Biology, Indiana University, Bloomington, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9014-5355","authenticated-orcid":true,"given":"Geoffrey J","family":"Barton","sequence":"additional","affiliation":[{"name":"School of Life Sciences, University of Dundee, Dundee, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6744-5889","authenticated-orcid":true,"given":"Gordon G","family":"Simpson","sequence":"additional","affiliation":[{"name":"School of Life Sciences, University of Dundee, Dundee, United Kingdom"},{"name":"The James Hutton Institute, Invergowrie, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"4374","published-online":{"date-parts":[[2021,4,27]]},"reference":[{"key":"bib1","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1016\/j.pbi.2019.04.007","article-title":"NLR singletons, pairs, and networks: evolution, assembly, and regulation of the intracellular immunoreceptor circuitry of plants","volume":"50","author":"Adachi","year":"2019","journal-title":"Current Opinion in Plant Biology"},{"key":"bib2","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1101\/gr.4137606","article-title":"Transcription-mediated gene fusion in the human genome","volume":"16","author":"Akiva","year":"2006","journal-title":"Genome Research"},{"key":"bib3","doi-asserted-by":"publisher","first-page":"2008","DOI":"10.1101\/gr.133744.111","article-title":"Detecting differential usage of exons from RNA-seq data","volume":"22","author":"Anders","year":"2012","journal-title":"Genome Research"},{"key":"bib4","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1038\/nrg3291","article-title":"The genetic basis of flowering responses to seasonal cues","volume":"13","author":"Andr\u00e9s","year":"2012","journal-title":"Nature Reviews Genetics"},{"key":"bib5","volume-title":"FastQC: a quality control tool for high throughput sequence data","author":"Andrews","year":"2010","unstructured":"Andrews S. 2010. 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