Project description: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 genes (NLRs) are found in plant genomes and provide 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 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 immunity.
Project description:Oxford Nanopore enables direct RNA sequencing allowing for base calling of RNA modifications. However, current direct RNA sequencing protocols may not be detecting some classes of non-coding RNAs such as SINE RNAs produced by Short Interspersed Nuclear Elements (SINEs). Using mouse hippocampi RNA samples, we have established a novel Nanopore direct RNA-seq protocol that in addition to long poly A selected RNAs allows sequencing also of non-poly A RNAs as well as short RNAs < 200nt (including SINE RNAs and other non poly A non coding RNAs). We provide here as a resource the first direct RNA-sequencing performed in mouse brain tissues that includes both mRNAs and non poly A or short non-coding RNAs such as SINEs.