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The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs [mRNA]

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE111238 | GEO | 2018/10/09

REPOSITORIES: GEO

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The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs [small RNA]

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.

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Temperature-sensitive sterility in rice determined by the dual role of AGO1d in phasiRNA biogenesis and function

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Phased secondary small interfering RNAs in Panax notoginseng

Project description:Recent results demonstrated that either non-coding or coding genes generate phased secondary small interfering RNAs (phasiRNAs) guided by specific miRNAs. Till now, there is no studies for phasiRNAs in Panax notoginseng (Burk.) F.H. Chen (P. notoginseng), an important traditional Chinese herbal medicinal plant species. Here we performed a genome-wide discovery of phasiRNAs and its host PHAS loci in P. notoginseng by analyzing small RNA sequencing profiles. Degradome sequencing profile was used to identify the trigger miRNAs of these phasiRNAs and potential targets of phasiRNAs. We also used RLM 5'-RACE to validate some of the identified phasiRNA targets. After analyzing 24 small RNA sequencing profiles of P. notoginseng, 204 and 90 PHAS loci that encoded 21 and 24 nucleotide (nt) phasiRNAs were identified. Furthermore, we found that phasiRNAs produced from some pentatricopeptide repeat-contain (PPR) genes target another layer of PPR genes as validated by both the degradome sequencing profile and RLM 5'-RACE analysis. We also find that miR171 with 21 nt triggers the 21 nt phasiRNAs from its conserved targets. We validated that some phasiRNAs generated from PPRs are functional by targeting other PPRs in trans. These results provide the first set of PHAS loci and phasiRNAs in P. notoginseng, and enhance our understanding of PHAS in plants.

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DCL4-Dependent Clusters of PhasiRNAs in Rice.

Project description:The osdcl4-1 mutant exhibits much severer developmental defects than dcl4 in Arabidopsis, suggesting that Os DCL4 may process broader substrates in rice. By deep sequencing of small RNAs from different tissues of wild types and osdcl4-1, we revealed that 21-nucleotide siRNAs were largely dependent on Os DCL4. Besides several tasiRNA loci reported in Arabidopsis and rice, over one thousand 21-nucleotide and several dozen 24-nucleotide phased siRNA (phasiRNA) clusters were identified in panicles but not in seedlings and grains. Further analyses identified two conserved 22-nucleotide motifs among the cleavage sites of the 21- and 24- phasiRNA loci, and the cleavage sites of over 90% of 21- and 24-nucleotide phasing clusters were confirmed by PARE/degradome analysis from 93-11 panicles. MiR2118 and miR2275, expressed specifically in panicles, were predicted to trigger cleavages at 21- and 24-nucleotide phasiRNA clusters, respectively. The triggers of phasiRNAs are more dependent on Os DCL4 than Os DCL1. Furthermore, the processing of 21-nucleotide phasiRNAs was largely Os DCL4-dependent, whereas the processing of 24-nucleotide phasiRNAs was slightly affected by Os DCL4, but not by Os DCL3a and Os DCL1. Our results revealed distinct roles of Os DCL4 in a novel 21- and 24-nucleotide phasiRNA biogenesis pathway in rice. Six small RNA libraries were constructed from seedlings and panicles of 93-11 (a wild-type Indica rice variety) and osdcl4-1, as well as those from Nipponbare panicles and seedlings (a wild-type Japonica rice variety).

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Secondary siRNAs from Medicago NB-LRRs modulated via miRNA-target interactions and their abundances

Project description:Small RNAs are a class of noncoding RNAs which are of great importance in gene expression regulatory networks. Different families of small RNAs are generated via distinct biogenesis pathways. One such family specific to plants is that of phased, secondary siRNAs (phasiRNAs); these require RDR6, DCL4, and microRNA (miRNA) trigger for their biogenesis. Protein-encoding genes are an important source of phasiRNAs. The model legume Medicago truncatula generates phasiRNAs from many PHAS loci, and we aimed to investigate their biogenesis and mechanism by which miRNAs trigger these molecules. We modulated miRNA abundances in transgenic tissues showing that the abundance of phasiRNAs correlates with the levels of both miRNA triggers and the target, precursor transcripts. We identified sets of phasiRNAs or PHAS loci that predominantly and substantially increase in response to miRNA overexpression. In the process of validating targets from miRNA overexpression tissues, we found that in the miRNA-mRNA target pairing, the 3’ terminal nucleotide (the 22nd position), but not the 10th position, is important for phasiRNA production. Mutating the single 3’ terminal nucleotide dramatically diminishes phasiRNA production. Ectopic expression of Medicago NB-LRR-targeting miRNAs in Arabidopsis showed that only a few NB-LRRs are capable of phasiRNA production; our data indicate that this is due to target inaccessibility determined by sequences flanking target sites. We propose that target accessibility is an important component of miRNA-target interactions that could be utilized in target prediction, and the evolution of mRNA sequences flanking miRNA target sites may be impacted.

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Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction (PARE)

Project description:Maize anthers, the male reproductive floral organs, express two classes of phased, small interfering RNAs (phasiRNAs). RNA profiling from ten sequential cohorts of staged maize anthers plus mature pollen revealed that 21-nt phased siRNAs (21-phasiRNAs) from 463 loci appear abruptly after germinal and initial somatic cell fate specification and then diminish, while 24-nt phased siRNAs (24-phasiRNAs) from 176 loci coordinately accumulate during meiosis and persist as haploid gametophytes differentiate into pollen. RNA sequencing of anther developmental mutants, together with in situ RNA hybridization detection of phasiRNA biogenesis factors, demonstrated that 21-phasiRNAs and 24-phasiRNAs are independently regulated. Furthermore, 21-phasiRNAs require epidermal cells while 24-phasiRNAs require functional tapetal cells. Maize phasiRNAs and mammalian PIWI-interacting RNAs (piRNAs) illustrate convergent evolution of small RNAs to support male reproduction. Examination of maize phasiRNAs by high throughput sequencing for RNA-seq, small RNA, and PARE profiling

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Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction (RNA-seq)

2015-02-11 | E-GEOD-52290 | biostudies-arrayexpress

Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction (small RNA-seq)

2015-02-11 | E-GEOD-52293 | biostudies-arrayexpress

DCL4-Dependent Clusters of PhasiRNAs in Rice.

2012-03-30 | GSE22763 | GEO

Endoplasmic reticulum as a hub organizing microRNAs and a subset of endogenous siRNAs in Arabidopsis [Ribo-Seq and RNA-Seq]

Project description:Endoplasmic reticulum (ER) was implicated as the site of microRNA (miRNA)-mediated translational repression in plants. Here, we examined the ER- and rough ER- associated small RNAome, transcriptome and translatome. We found that nearly all cellular transcripts were present on membrane-bound polysomes (MBPs), and miRNAs and a small set of endogenous siRNAs were particularly enriched on MBPs. The MBP- enriched miRNAs and siRNAs associated with, and were recruited to membranes by, their effector protein ARGONAUTE1 (AGO1). AGO1 associated with ER in a partly RNA-independent manner. Reduced membrane association of 22-nt miRNAs, which trigger the biogenesis of phased, secondary siRNAs (phasiRNAs) from their target transcripts, was accompanied by decreased production or loss of phasing of phasiRNAs. The phasiRNA precursor transcripts, previously thought to be noncoding, were associated with MBPs in a manner that supported phasiRNA production. These findings point to the ER as a hub that hosts and organizes endogenous small RNAs in plants.

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