scholarly journals RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

2013 ◽  
Vol 14 (2) ◽  
pp. 100-112 ◽  
Author(s):  
Stephane E. Castel ◽  
Robert A. Martienssen
Keyword(s):  
Rna Interference ◽  
Small Rnas

RNA Interference Mechanisms and Applications in Plant Pathology

2018 ◽  
Vol 56 (1) ◽  
pp. 581-610 ◽  
Author(s):  
Cristina Rosa ◽  
Yen-Wen Kuo ◽  
Hada Wuriyanghan ◽  
Bryce W. Falk
Keyword(s):  
Plant Pathology ◽  
Rna Interference ◽  
Gene Function ◽  
Small Rnas ◽  
Plant Pathogens ◽  
Common Ancestor ◽  
Plant Protection ◽  
Plant Diseases ◽  
Antiviral Defense ◽  
Endogenous Genes

The origin of RNA interference (RNAi), the cell sentinel system widely shared among eukaryotes that recognizes RNAs and specifically degrades or prevents their translation in cells, is suggested to predate the last eukaryote common ancestor ( 138 ). Of particular relevance to plant pathology is that in plants, but also in some fungi, insects, and lower eukaryotes, RNAi is a primary and effective antiviral defense, and recent studies have revealed that small RNAs (sRNAs) involved in RNAi play important roles in other plant diseases, including those caused by cellular plant pathogens. Because of this, and because RNAi can be manipulated to interfere with the expression of endogenous genes in an intra- or interspecific manner, RNAi has been used as a tool in studies of gene function but also for plant protection. Here, we review the discovery of RNAi, canonical mechanisms, experimental and translational applications, and new RNA-based technologies of importance to plant pathology.

scholarly journals Unusual characteristics of dicistrovirus-derived small RNAs in the small brown planthopper, Laodelphax striatellus

2014 ◽  
Vol 95 (3) ◽  
pp. 712-718 ◽  
Author(s):  
Junmin Li ◽  
Ida Bagus Andika ◽  
Yanru Zhou ◽  
Jiangfeng Shen ◽  
Zongtao Sun ◽  
...  
Keyword(s):  
Rna Interference ◽  
Small Rna ◽  
Small Rnas ◽  
Viral Genome ◽  
Size Range ◽  
Brown Planthopper ◽  
Insect Vector ◽  
Laodelphax Striatellus ◽  
Sense Strand ◽  
Wide Size Distribution

In this study, sequences of small RNA (sRNA) libraries derived from the insect vector Laodelphax striatellus were assembled into contigs and used as queries for database searches. A large number of contigs were highly homologous to the genome sequence of an insect dicistrovirus, himetobi P virus (HiPV). Interestingly, HiPV-derived sRNAs had a wide size distribution, and were relatively abundant throughout the 18–30 nt size range with only a slight peak at 22 nt. HiPV sRNAs had a strong bias towards the sense strand, whilst the antisense sRNAs were predominantly 21 and 22 nt. HiPV sRNAs do not have the typical features of PIWI-interacting RNAs, but their 3′ ends were preferentially cleaved at UA-rich sequences. Our data suggest that HiPV sRNAs may be derived both from activities of the RNA interference pathway and from cleavage of the viral genome by other host RNases.

scholarly journals Diversity of RNA interference pathways in regulation of endogenous and exogenous sequences expression in ciliates Tetrahymena and Paramecium

2019 ◽  
Vol 17 (2) ◽  
pp. 113-125
Author(s):  
Irina V. Nekrasova ◽  
Alexey A. Potekhin
Keyword(s):  
Rna Interference ◽  
Environmental Conditions ◽  
Small Rnas ◽  
Nucleotide Sequences ◽  
Vegetative Cells ◽  
Homologous Sequences ◽  
Different Types ◽  
External Stimuli

RNA interference plays a major role in biology of ciliates. Diverse small RNAs regulate many processes in vegetative cells of ciliates Tetrahymena and Paramecium. Different types of endogenous and exogenous nucleotide sequences induce different RNAi pathways resulting in silencing of the homologous sequences in the macronuclear genome. Likely this way ciliates are able to quickly inactivate heterogeneous sequences and to adapt efficiently to the environmental conditions and external stimuli.

scholarly journals RNA interference in formation of the somatic genome of ciliates Paramecium and Tetrahymena

2018 ◽  
Vol 16 (4) ◽  
pp. 5-22
Author(s):  
Irina V. Nekrasova ◽  
Alexey A. Potekhin
Keyword(s):  
Rna Interference ◽  
Small Rnas ◽  
Generative Nucleus ◽  
Genome Scanning ◽  
Somatic Genome ◽  
Sexual Progeny

Ciliates are the model of choice to study RNA interference, the mechanism playing key role in biology of these protists. The genome scanning processes of two ciliates, Tetrahymena and Paramecium (Oligohymenophorea), leading to formation of the somatic genome from the chromosomes of the generative nucleus are compared in the review. Matching of several simulta neously present in one cell genomes is mediated by small RNAs and results in precise reproduction of maternal somatic genome in the sexual progeny.

scholarly journals Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes

2017 ◽  
Author(s):  
Fergal M. Waldron ◽  
Graham N. Stone ◽  
Darren J. Obbard
Keyword(s):  
Rna Interference ◽  
Small Rnas ◽  
Brown Alga ◽  
Length Distribution ◽  
Rnai Pathway ◽  
Metagenomic Sequencing ◽  
Wild Type ◽  
Distinctive Group ◽  
Animal Phyla ◽  
Rnai Response

AbstractRNA interference (RNAi)-related pathways target viruses and transposable element (TE) transcripts in plants, fungi, and ecdysozoans (nematodes and arthropods), giving protection against infection and transmission. In each case, this produces abundant TE and virus-derived 20-30nt small RNAs, which provide a characteristic signature of RNAi-mediated defence. The broad phylogenetic distribution of the Argonaute and Dicer-family genes that mediate these pathways suggests that defensive RNAi is ancient and probably shared by most animal (metazoan) phyla. Indeed, while vertebrates had been thought an exception, it has recently been argued that mammals also possess an antiviral RNAi pathway, although its immunological relevance is currently uncertain and the viral small RNAs are not detectably under natural conditions. Here we use a metagenomic approach to test for the presence of virus-derived small RNAs in five divergent animal phyla (Porifera, Cnidaria, Echinodermata, Mollusca, and Annelida), and in a brown alga—which represents an independent origin of multicellularity from plants, fungi, and animals. We use metagenomic RNA sequencing to identify around 80 virus-like contigs in these lineages, and small RNA sequencing to identify small RNAs derived from those viruses. Contrary to our expectations, we were unable to identify canonical (i.e. Drosophila-, nematode- or plant-like) viral small RNAs in any of these organisms, despite the widespread presence of abundant micro-RNAs, and transposon-derived somatic Piwi-interacting piRNAs in the animals. Instead, we identified a distinctive group of virus-derived small RNAs in the mollusc, which have a piRNA-like length distribution but lack key signatures of piRNA biogenesis, and a group of 21U virus-derived small RNAs in the brown alga. We also identified primary piRNAs derived from putatively endogenous copies of DNA viruses in the cnidarian and the echinoderm, and an endogenous RNA virus in the mollusc. The absence of canonical virus-derived small RNAs from our samples may suggest that the majority of animal phyla lack an antiviral RNAi response. Alternatively, these phyla could possess an antiviral RNAi response resembling that reported for vertebrates, which is not detectable through simple metagenomic sequencing of wild-type individuals. In either case, our findings suggest that the current antiviral RNAi responses of arthropods and nematodes are highly diverged from the ancestral metazoan state, and that antiviral RNAi may even have evolved independently on multiple occasions.Author summaryThe presence of abundant virus-derived small RNAs in infected plants, fungi, nematodes, and arthropods suggests that Dicer-dependent antiviral RNAi is an ancient and conserved defence. Using metagenomic sequencing from wild-caught organisms we show that antiviral RNAi is highly variable across animals. We identify a distinctive group of virus-derived small RNAs in a mollusc, which have a piRNA-like length distribution but lack key signatures of piRNA biogenesis. We also report a group of 21U virus-derived small RNAs in a brown alga, which represents an origin of multicellularity separate from that of plants, fungi, and animals. The absence of virus-derived small RNAs from our samples may suggest that the majority of animal phyla lack an antiviral RNAi response or that these phyla could possess an antiviral RNAi response resembling that reported for vertebrates, which is not detectable through simple metagenomic sequencing of wild-type individuals. In addition, we report abundant somatic piRNAs across anciently divergent animals suggesting that this is the ancestral state in Bilateria. Our study challenges the widely-held assumption that most invertebrates possess an antiviral RNAi pathway likely similar to that seen in Drosophila, other arthropods, and nematodes.

Distinct Populations of Primary and Secondary Effectors During RNAi in C. elegans

Science ◽  
2006 ◽  
Vol 315 (5809) ◽  
pp. 241-244 ◽  
Author(s):  
Julia Pak ◽  
Andrew Fire
Keyword(s):  
Rna Interference ◽  
Small Rnas ◽  
De Novo ◽  
Messenger Rnas ◽  
Cellular Regulation ◽  
Rdrp Activity ◽  
Antisense Transcripts ◽  
Double Stranded Rna ◽  
C Elegans ◽  
Secondary Sirnas

RNA interference (RNAi) is a phylogenetically widespread gene-silencing process triggered by double-stranded RNA. In plants and Caenorhabditis elegans, two distinct populations of small RNAs have been proposed to participate in RNAi: “Primary siRNAs” (derived from DICER nuclease-mediated cleavage of the original trigger) and “secondary siRNAs” [additional small RNAs whose synthesis requires an RNA-directed RNA polymerase (RdRP)]. Analyzing small RNAs associated with ongoing RNAi in C. elegans, we found that secondary siRNAs constitute the vast majority. The bulk of secondary siRNAs exhibited structure and sequence indicative of a biosynthetic mode whereby each molecule derives from an independent de novo initiation by RdRP. Analysis of endogenous small RNAs indicated that a fraction derive from a biosynthetic mechanism that is similar to that of secondary siRNAs formed during RNAi, suggesting that small antisense transcripts derived from cellular messenger RNAs by RdRP activity may have key roles in cellular regulation.

scholarly journals H3K9me3 is Required for Inheritance of Small RNAs that Target a Unique Subset of Newly Evolved Genes

2018 ◽  
Author(s):  
Itamar Lev ◽  
Hila Gingold ◽  
Oded Rechavi
Keyword(s):  
Rna Interference ◽  
Caenorhabditis Elegans ◽  
Small Rnas ◽  
Foreign Gene ◽  
Small Interfering Rnas ◽  
Endogenous Gene ◽  
C Elegans ◽  
Histone 3 ◽  
Repressive Chromatin ◽  
Genome Wide

AbstractIn Caenorhabditis elegans, RNA interference (RNAi) responses can transmit across generations via small RNAs. RNAi inheritance is associated with Histone-3-Lysine-9 tri-methylation (H3K9me3) of the targeted genes. In other organisms, maintenance of silencing requires a feed-forward loop between H3K9me3 and small RNAs. Here we show that in C. elegans not only is H3K9me3 unnecessary for inheritance, the modification’s function depends on the identity of the RNAi-targeted gene. We found an asymmetry in the requirement for H3K9me3 and the main worm H3K9me3 methyltransferases, SET-25 and SET-32. Both methyltransferases promote heritable silencing of the foreign gene gfp, but are dispensable for silencing of the endogenous gene oma-1. Genome-wide examination of heritable endogenous small interfering RNAs (endo-siRNAs) revealed that the SET-25-dependent heritable endo-siRNAs target newly acquired and highly H3K9me3 marked genes. Thus, “repressive” chromatin marks could be important specifically for heritable silencing of genes which are flagged as “foreign”, such as gfp.

scholarly journals piRNAs prevent runaway amplification of siRNAs from ribosomal RNAs and histone mRNAs

2020 ◽  
Author(s):  
Brooke E. Montgomery ◽  
Tarah Vijayasarathy ◽  
Taylor N. Marks ◽  
Kailee J. Reed ◽  
Taiowa A. Montgomery
Keyword(s):  
Rna Interference ◽  
Small Rnas ◽  
Rnai Pathway ◽  
Specific Class ◽  
Biological Processes ◽  
Small Interfering Rnas ◽  
Ribosomal Rnas ◽  
Feed Forward ◽  
Histone Mrnas ◽  
Low Levels

ABSTRACTPiwi-interacting RNAs (piRNAs) are a largely germline-specific class of small RNAs found in animals. Although piRNAs are best known for silencing transposons, they regulate many different biological processes. Here we identify a role for piRNAs in preventing runaway amplification of small interfering RNAs (siRNAs) from certain genes, including ribosomal RNAs (rRNAs) and histone mRNAs. In Caenorhabditis elegans, rRNAs and some histone mRNAs are heavily targeted by piRNAs, which facilitates their entry into an endogenous RNA interference (RNAi) pathway involving a class of siRNAs called 22G-RNAs. Under normal conditions, rRNAs and histone mRNAs produce relatively low levels of 22G-RNAs. But if piRNAs are lost, 22G-RNA production is highly elevated. We show that 22G-RNAs produced downstream of piRNAs likely function in a feed-forward amplification circuit. Thus, our results suggest that piRNAs facilitate low-level 22G-RNA production while simultaneously obstructing the 22G-RNA machinery to prevent runaway amplification from certain RNAs. Histone mRNAs and rRNAs are unique from other cellular RNAs in lacking polyA tails, which may promote feed-forward amplification of 22G-RNAs. In support of this, we show that the subset of histone mRNAs that contain polyA tails are largely resistant to silencing in piRNA mutants.

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