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

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

PROVIDER: PRJNA436260 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7761230.fastq.gz	Fastqsanger.gz
	SRR7761240.fastq.gz	Fastqsanger.gz
	SRR7761231.fastq.gz	Fastqsanger.gz
	SRR7761241.fastq.gz	Fastqsanger.gz
	SRR7761232.fastq.gz	Fastqsanger.gz

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

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

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

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

| PRJNA436256 | ENA

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

2018-10-09 | GSE111239 | GEO

The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs in Arabidopsis

Project description:The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs in Arabidopsis

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The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs.

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.

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piRNA-guided slicing specifies transcripts for Zucchini dependent, phased piRNA biogenesis

Project description:PIWI-clade Argonaute proteins repress transposable elements in animal gonads. Their sequence specificity is conferred via bound ~23-30nt long piRNAs, which are processed from single stranded precursor RNAs. How transcripts are specified as precursors and processed into stereotypical piRNA populations are central unresolved questions. Here we show that piRNA-guided RNA cleavage in Drosophila results not only in generation of a ping-pong partner piRNA but further triggers efficient 3′ directed and phased primary piRNA biogenesis. Phasing is a feature of primary piRNAs in somatic and germline cells and a consequence of consecutive endo-nucleolytic cleavage events catalyzed by Zucchini. Formation of 3′ and 5′ ends of flanking piRNAs is therefore tightly coupled. Zucchini also participates in 3′ end formation of secondary piRNAs but its function can be bypassed by additional downstream piRNA-guided cleavages and subsequent precursor trimming. Hallmarks of Zucchini-dependent phased piRNA biogenesis are also evident in mouse testes, pointing to an evolutionarily conserved mechanism of piRNA biogenesis. This study aims at understanding how piRNA biogenesis is intiated in the Drosophila germline and understanding the role of the nuclease Zucchini/MitoPLD in piRNA biogenesis in Drosophila/Mouse by analysing small RNA sequencing data of various genotypes and sensor constructs.

2015-06-07 | E-GEOD-64802 | biostudies-arrayexpress

piRNA-guided slicing specifies transcripts for Zucchini dependent, phased piRNA biogenesis

2015-06-07 | GSE64802 | GEO

The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs in Arabidopsis

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-10-09 | GSE111240 | GEO

Biogenesis of phased siRNAs on membrane-bound polysomes in Arabidopsis.

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.

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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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