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Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Phytophthora ramorum Phytophthora infestans Phytophthora sojae

PROVIDER: GSE50033 | GEO | 2013/10/21

SECONDARY ACCESSION(S): PRJNA215842

REPOSITORIES: GEO

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Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs.

Project description:In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora species belong to a phylogenetically distinct group of economically important plant pathogens that cause billions of dollars in yield losses annually as well as ecologically devastating outbreaks. We analyzed the small RNA-generating components of the genomes of P. infestans, P. sojae and P. ramorum using bioinformatics, genetic, phylogenetic and high-throughput sequencing-based methods. Each species produces two distinct populations of small RNAs that are predominantly 21- or 25-nucleotides long. The 25-nucleotide small RNAs were primarily derived from loci encoding transposable elements and we propose that these small RNAs define a pathway of short-interfering RNAs that silence repetitive genetic elements. The 21-nucleotide small RNAs were primarily derived from inverted repeats, including a novel microRNA family that is conserved among the three species, and several gene families, including Crinkler effectors and type III fibronectins. The Phytophthora microRNA is predicted to target a family of amino acid/auxin permeases, and we propose that 21-nucleotide small RNAs function at the post-transcriptional level. The functional significance of microRNA-guided regulation of amino acid/auxin permeases and the association of 21-nucleotide small RNAs with Crinkler effectors remains unclear, but this work provides a framework for testing the role of small RNAs in Phytophthora biology and pathogenesis in future work.

| S-EPMC3804510 | biostudies-literature

Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-10-21 | E-GEOD-50033 | biostudies-arrayexpress

Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora sojae small RNA

Project description:Deep sequencing of small RNAs from three Phytophthora species, P. infestans, P. ramorum and P. sojae, was done to systematically analyze small RNA-generating components of Phytophthora genomes. We found that each species produces two distinct small RNA populations that are predominantly 21- or 25-nucleotides long. We present evidence that 25-nucleotide small RNAs are short-interfering RNAs that silence repetitive genetic elements. In contrast, 21-nucleotide small RNAs are associated with inverted repeats, including a novel microRNA family, and may function at the post-transcriptional level.

2013-10-21 | GSE50032 | GEO

Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora ramorum small RNA

2013-10-21 | GSE50031 | GEO

Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora infestans small RNA

2013-10-21 | GSE50030 | GEO

Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora sojae small RNA

2013-10-21 | E-GEOD-50032 | biostudies-arrayexpress

Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora ramorum small RNA

2013-10-21 | E-GEOD-50031 | biostudies-arrayexpress

Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora infestans small RNA

2013-10-21 | E-GEOD-50030 | biostudies-arrayexpress

An endogenous small interfering RNA pathway in Drosophila.

Project description:Drosophila endogenous small RNAs are categorized according to their mechanisms of biogenesis and the Argonaute protein to which they bind. MicroRNAs are a class of ubiquitously expressed RNAs of approximately 22 nucleotides in length, which arise from structured precursors through the action of Drosha-Pasha and Dicer-1-Loquacious complexes. These join Argonaute-1 to regulate gene expression. A second endogenous small RNA class, the Piwi-interacting RNAs, bind Piwi proteins and suppress transposons. Piwi-interacting RNAs are restricted to the gonad, and at least a subset of these arises by Piwi-catalysed cleavage of single-stranded RNAs. Here we show that Drosophila generates a third small RNA class, endogenous small interfering RNAs, in both gonadal and somatic tissues. Production of these RNAs requires Dicer-2, but a subset depends preferentially on Loquacious rather than the canonical Dicer-2 partner, R2D2 (ref. 14). Endogenous small interfering RNAs arise both from convergent transcription units and from structured genomic loci in a tissue-specific fashion. They predominantly join Argonaute-2 and have the capacity, as a class, to target both protein-coding genes and mobile elements. These observations expand the repertoire of small RNAs in Drosophila, adding a class that blurs distinctions based on known biogenesis mechanisms and functional roles.

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The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs.

Project description:In contrast to microRNAs and Piwi-associated RNAs, short interfering RNAs (siRNAs) are seemingly dispensable for host-directed gene regulation in Drosophila. This notion is based on the fact that mutants lacking the core siRNA-generating enzyme Dicer-2 or the predominant siRNA effector Argonaute 2 are viable, fertile and of relatively normal morphology. Moreover, endogenous Drosophila siRNAs have not yet been identified. Here we report that siRNAs derived from long hairpin RNA genes (hpRNAs) programme Slicer complexes that can repress endogenous target transcripts. The Drosophila hpRNA pathway is a hybrid mechanism that combines canonical RNA interference factors (Dicer-2, Hen1 (known as CG12367) and Argonaute 2) with a canonical microRNA factor (Loquacious) to generate approximately 21-nucleotide siRNAs. These novel regulatory RNAs reveal unexpected complexity in the sorting of small RNAs, and open a window onto the biological usage of endogenous RNA interference in Drosophila.

| S-EPMC2735555 | biostudies-literature

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