GSE111239
The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs [small RNA]
Plants evolved an array of disease resistance genes (R genes) to fight pathogens. In the absence of pathogen infection, NBS-LRR genes, which comprise a major subfamily of R genes, are suppressed by a small RNA cascade involving microRNAs (miRNAs) that trigger the biogenesis of phased siRNAs (phasiRNAs) from R gene transcripts. However, whether or how R genes influence small RNA biogenesis is unknown. In this study, we isolated a mutant with global defects in the biogenesis of miRNAs and phasiRNAs in Arabidopsis thaliana and traced the defects to the over accumulation and nuclear localization of an R protein SNC1. We showed that nuclear SNC1 represses the transcription of miRNA and phasiRNA loci, probably through the transcriptional corepressor TPR1. Intriguingly, nuclear SNC1 reduces the accumulation of phasiRNAs from three source R genes and concomitantly, the expression of a majority of the ~170 R genes was up-regulated. Taken together, this study reveals a new R gene-miRNA-phasiRNA regulatory module that regulates plants' growth-defense trade-off. Overall design: For library construction, 30 µg total RNA was resolved on a 15% polyacrylamide gel with 8 M urea. Small RNAs in the 15~40 nt size range were recovered as described 48. Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Libraty Prep Set for Illumina (New England Biolabs, E7300), and sequenced with an Illumina HiSeq2500 platform at BerryGenomics, China. Raw reads (SE50) were trimmed using Perl scripts to remove adapters. The clean reads were mapped to the Arabidopsis thaliana genome TAIR10 using the Bowtie program 49. The small RNA reads were calculated and normalized in RPM (reads per million mapped reads). The comparison between samples was conducted with the R package edgeR 50. For analysis of miRNA levels, small RNA reads were mapped to annotated miRNAs in miRBase v21. For analysis of tasiRNAs levels, small RNA reads were mapped to each of the eight annotated TAS genes (TAS1A/1B/1C, TAS2, TAS3A/3B/3C and TAS4). For the analysis of phasiRNAs from protein coding genes, such as R genes and PPR genes, small RNA reads were mapped to the genes known to produce phasiRNAs and only uniquely mapped reads were included in subsequent analyses.