Similar Datasets
Project description: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 isolate a mutant with global defects in the biogenesis of miRNAs and phasiRNAs in Arabidopsis thaliana and trace the defects to the over accumulation and nuclear localization of an R protein SNC1. We show 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 ~170R genes is up-regulated. Taken together, this study suggests an R gene-miRNA-phasiRNA regulatory module that amplifies plant immune responses.
| S-EPMC6265325 | biostudies-literature
Project description: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.
2018-10-09 | GSE111238 | GEO
Project description: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.
2018-10-09 | GSE111239 | GEO
Project description:The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs in Arabidopsis
| PRJNA436243 | ENA
Project description:The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs [mRNA]
| PRJNA436256 | ENA
Project description:Small RNAs are central players in RNA silencing, yet their cytoplasmic compartmentalization and the effects it may have on their activities have not been studied at the genomic scale. Here we report that Arabidopsis microRNAs (miRNAs) and small interfering RNAs (siRNAs) are distinctly partitioned between the endoplasmic reticulum (ER) and cytosol. All miRNAs are associated with membrane-bound polysomes (MBPs) as opposed to polysomes in general. The MBP association is functionally linked to a deeply conserved and tightly regulated activity of miRNAs - production of phased siRNAs (phasiRNAs) from select target RNAs. The phasiRNA precursor RNAs, thought to be noncoding, are on MBPs and are occupied by ribosomes in a manner that supports miRNA-triggered phasiRNA production, suggesting that ribosomes on the rough ER impact siRNA biogenesis. This study reveals global patterns of cytoplasmic partitioning of small RNAs and expands the known functions of ribosomes and ER.
| S-EPMC5207768 | biostudies-literature
Project description:The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs [small RNA]
| PRJNA436260 | ENA
Project description:The Arabidopsis genes, TAS2 and TAS1a, produce structurally similar noncoding transcripts that are transformed into short (21-nucleotide [nt]) and long (24-nt) siRNAs by RNA silencing pathways. Some of these short siRNAs direct the cleavage of protein-coding transcripts, and thus function as trans-acting siRNAs (ta-siRNAs). Using genetic analysis, we defined the pathway by which ta-siRNAs and other short siRNAs are generated from these loci. This process is initiated by the miR173-directed cleavage of a primary poly(A) transcript. The 3' fragment is then transformed into short siRNAs by the sequential activity of SGS3, RDR6, and DCL4: SGS3 stabilizes the fragment, RDR6 produces a complementary strand, and DCL4 cleaves the resulting double-stranded molecule into short siRNAs, starting at the end with the miR173 cleavage site and proceeding in 21-nt increments from this point. The 5' cleavage fragment is also processed by this pathway, but less efficiently. The DCL3-dependent pathway that generates long siRNAs does not require miRNA-directed cleavage and plays a minor role in the silencing of these loci. Our results define the core components of a post-transcriptional gene silencing pathway in Arabidopsis and reveal some of the features that direct transcripts to this pathway.
| S-EPMC1221887 | biostudies-literature
Project description:Phased siRNAs (phasiRNAs) are a class of small interfering RNAs (siRNAs) which play essential roles in plant development and defence. However, only a few phasiRNAs have been extensively studied due to the difficulties in identifying and characterizing plant phasiRNAs by plant biologists. Herein, we describe a comprehensive and multi-functional web server termed PhasiRNAnalyzer, which is able to identify all crucial components in plant phasiRNA's regulatory pathway (phase-initiator→PHAS gene→phasiRNA cluster→target gene). Currently, PhasiRNAnalyzer exhibits the following advantages: I) It is the most comprehensive platform which hosts 170 plant species with 256 genome data, 438 cDNA data and 271 degradome data. II) It can identify all crucial components in phasiRNA's regulatory pathway, and verify the interactions between phasiRNAs and their target genes based on degradome data. III) It can perform differential expression analysis of phasiRNAs on each PHAS gene locus between different samples conveniently. IV) It provides the user-friendly interfaces and introduces several improvements, primarily by making more accurate and efficient analysis when dealing with deep sequencing data. In summary, PhasiRNAnalyzer is a comprehensive and systemic phasiRNA analysis server with high sensitivity and efficiency. It can be freely accessed at https://cbi.njau.edu.cn/PPSA/.
| S-EPMC8594884 | biostudies-literature
Project description:DNA methylation directed by 24-nucleotide (nt) small interfering RNAs (siRNAs) plays critical roles in gene regulation and transposon silencing in Arabidopsis. 24-nt siRNAs are known to be processed from double-stranded RNAs by Dicer-like 3 (DCL3) and loaded into the effector Argonaute 4 (AGO4). Here we report a distinct class of siRNAs independent of DCLs (sidRNAs). sidRNAs are present as ladders of ? 20-60 nt in length, often having the same 5' ends but differing in 3' ends by 1-nt steps. We further show that sidRNAs are associated with AGO4 and capable of directing DNA methylation. Finally we show that sidRNA production depends on distributive 3'-5' exonucleases. Our findings suggest an alternative route for siRNA biogenesis. Precursor transcripts are bound by AGO4 and subsequently subjected to 3'-5' exonucleolytic trimming for maturation. We propose that sidRNAs generated through this route are the initial triggers of de novo DNA methylation.
| S-EPMC5110219 | biostudies-literature