The long hand of the small RNAs reaches into several levels of gene regulation

2004 ◽  
Vol 82 (4) ◽  
pp. 472-481 ◽  
Author(s):  
Tony Nolan ◽  
Carlo Cogoni
Keyword(s):  
Gene Silencing ◽  
Small Rnas ◽  
Developmental Regulation ◽  
Transcriptional Gene Silencing ◽  
Rna Molecules ◽  
New Class ◽  
Post Transcriptional Gene Silencing ◽  
Wide Range ◽  
Cellular Defence ◽  
Genomic Organisation

Small RNA molecules such as siRNAs and miRNAs represent a new class of molecules that have been implicated in a wide range of diverse gene silencing phenomena. It is now becoming clear that these two similar molecules share several common features in both their biogenesis and their mechanism of action. Thus, the siRNA and miRNA pathways may have evolved from a common ancestral mechanism that has diverged to play important roles in developmental regulation, genomic organisation, and cellular defence against foreign nucleic acids.Key words: miRNA, siRNA, post-transcriptional gene silencing, RNAi, heterochromatin.

scholarly journals Virus and Viroid-Derived Small RNAs as Modulators of Host Gene Expression: Molecular Insights Into Pathogenesis

2021 ◽  
Vol 11 ◽  
Author(s):  
S. V. Ramesh ◽  
Sneha Yogindran ◽  
Prabu Gnanasekaran ◽  
Supriya Chakraborty ◽  
Stephan Winter ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Small Rnas ◽  
Rna Silencing ◽  
Transcriptional Gene Silencing ◽  
Genomic Rnas ◽  
Post Transcriptional Gene Silencing ◽  
Viroid Infection ◽  
Wide Range ◽  
Associated Symptoms ◽  
Sequence Complementarity

Virus-derived siRNAs (vsiRNAs) generated by the host RNA silencing mechanism are effectors of plant’s defense response and act by targeting the viral RNA and DNA in post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) pathways, respectively. Contrarily, viral suppressors of RNA silencing (VSRs) compromise the host RNA silencing pathways and also cause disease-associated symptoms. In this backdrop, reports describing the modulation of plant gene(s) expression by vsiRNAs via sequence complementarity between viral small RNAs (sRNAs) and host mRNAs have emerged. In some cases, silencing of host mRNAs by vsiRNAs has been implicated to cause characteristic symptoms of the viral diseases. Similarly, viroid infection results in generation of sRNAs, originating from viroid genomic RNAs, that potentially target host mRNAs causing typical disease-associated symptoms. Pathogen-derived sRNAs have been demonstrated to have the propensity to target wide range of genes including host defense-related genes, genes involved in flowering and reproductive pathways. Recent evidence indicates that vsiRNAs inhibit host RNA silencing to promote viral infection by acting as decoy sRNAs. Nevertheless, it remains unclear if the silencing of host transcripts by viral genome-derived sRNAs are inadvertent effects due to fortuitous pairing between vsiRNA and host mRNA or the result of genuine counter-defense strategy employed by viruses to enhance its survival inside the plant cell. In this review, we analyze the instances of such cross reaction between pathogen-derived vsiRNAs and host mRNAs and discuss the molecular insights regarding the process of pathogenesis.

scholarly journals An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection

2021 ◽  
Author(s):  
Ganna Reshetnyak ◽  
Jonathan M. Jacobs ◽  
Florence Auguy ◽  
Coline Sciallano ◽  
Lisa Claude ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Stress Responses ◽  
Small Rnas ◽  
Early Stage ◽  
Kinase Domain ◽  
Transcriptional Gene Silencing ◽  
Small Interfering Rnas ◽  
Post Transcriptional Gene Silencing ◽  
Virulent Strains ◽  
Microbe Interactions

ABSTRACTNon-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant-microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20-22nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences often encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and some xisRNA loci coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. xisRNA induction possibly mediates post-transcriptional gene silencing but they do not broadly suppress cis-genes expression on the basis of mRNA-seq data. Overall, our results identify a group of unusual sRNAs with a potential role in plant-microbe interactions.

Host-induced gene silencing and spray-induced gene silencing for crop protection against viruses.

2021 ◽  
pp. 72-85
Author(s):  
Angela Ricci ◽  
Silvia Sabbadini ◽  
Laura Miozzi ◽  
Bruno Mezzetti ◽  
Emanuela Noris
Keyword(s):  
Gene Silencing ◽  
Plant Pathogens ◽  
Crop Protection ◽  
Plant Defence ◽  
Transcriptional Gene Silencing ◽  
Target Sequence ◽  
Sequence Specificity ◽  
Rna Molecules ◽  
Political Concern ◽  
Post Transcriptional Gene Silencing

Abstract Since the beginning of agriculture, plant virus diseases have been a strong challenge for farming. Following its discovery at the very beginning of the 1990s, the RNA interference (RNAi) mechanism has been widely studied and exploited as an integrative tool to obtain resistance to viruses in several plant species, with high target-sequence specificity. In this chapter, we describe and review the major aspects of host-induced gene silencing (HIGS), as one of the possible plant defence methods, using genetic engineering techniques. In particular, we focus our attention on the use of RNAi-based gene constructs to introduce stable resistance in host plants against viral diseases, by triggering post-transcriptional gene silencing (PTGS). Recently, spray-induced gene silencing (SIGS), consisting of the topical application of small RNA molecules to plants, has been explored as an alternative tool to the stable integration of RNAi-based gene constructs in plants. SIGS has great and innovative potential for crop defence against different plant pathogens and pests and is expected to raise less public and political concern, as it does not alter the genetic structure of the plant.

scholarly journals Dual-layer transposon repression in heads of Drosophila melanogaster

2018 ◽  
Author(s):  
Marius van den Beek ◽  
Bruno da Silva ◽  
Juliette Pouch ◽  
Mohammed el amine Ali Chaouche ◽  
Clément Carré ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Gene Silencing ◽  
Rna Extraction ◽  
Transcript Abundance ◽  
Transcriptional Gene Silencing ◽  
Loss Of Function ◽  
Wild Type ◽  
Rna Molecules ◽  
Post Transcriptional Gene Silencing ◽  
Ping Pong

AbstractpiRNA-mediated repression of transposable elements (TE) in the germline limits the accumulation of heritable mutations caused by their transposition in the genome. It is not clear whether the piRNA pathway plays a functional role in adult, non-gonadal tissues in Drosophila melanogaster. To address this question, we first analyzed the small RNA content of adult Drosophila melanogaster heads. We found that varying amount of piRNA-sized, ping-pong positive molecules in heads correlates with contamination by gonadal tissue during RNA extraction, suggesting that most of piRNAs detected in head sequencing libraries originate from gonads. We next sequenced the heads of wild type and piwi mutants to address whether piwi loss of function would affect the low amount of piRNA-sized, ping-pong negative molecules that are still detected in heads hand-checked to avoid gonadal contamination. We find that loss of piwi does not affect significantly these 24-28 RNA molecules. Instead, we observe increased siRNA levels against the majority of Drosophila transposable element families. To determine the effect of this siRNA level change on transposon expression, we sequenced the transcriptome of wild type, piwi, dicer-2 and piwi, dicer-2 double-mutant fly heads. We find that RNA expression levels of the majority of TE families in piwi or dicer-2 mutants remain unchanged and that TE transcript abundance increases significantly only in piwi, dicer-2 double-mutants. These results lead us to suggest a dual-layer model for TE repression in adult somatic tissues. Piwi-mediated transcriptional gene silencing (TGS) established during embryogenesis constitutes the first layer of TE repression whereas Dicer-2-dependent siRNA-mediated post-transcriptional gene silencing (PTGS) provide a backup mechanism to repress TEs that escape silencing by piwi-mediated TGS.

scholarly journals The Diversity of Plant Small RNAs Silencing Mechanisms

2019 ◽  
Vol 73 (5) ◽  
pp. 362-367 ◽  
Author(s):  
Jens A. Schröder ◽  
Pauline E. Jullien
Keyword(s):  
Gene Regulation ◽  
Gene Silencing ◽  
Small Rna ◽  
Small Rnas ◽  
Genome Stability ◽  
Molecular Mechanisms ◽  
Transcriptional Gene Silencing ◽  
Regulation Mechanism ◽  
Regulatory Processes ◽  
Post Transcriptional Gene Silencing

Small RNAs gene regulation was first discovered about 20 years ago. It represents a conserve gene regulation mechanism across eukaryotes and is associated to key regulatory processes. In plants, small RNAs tightly regulate development, but also maintain genome stability and protect the plant against pathogens. Small RNA gene regulation in plants can be divided in two canonical pathways: Post-transcriptional Gene Silencing (PTGS) that results in transcript degradation and/or translational inhibition or Transcriptional Gene Silencing (TGS) that results in DNA methylation. In this review, we will focus on the model plant Arabidopsis thaliana. We will provide a brief overview of the molecular mechanisms involved in canonical small RNA pathways as well as introducing more atypical pathways recently discovered.

RNA duplexes in transcriptional regulation

2010 ◽  
Vol 1 (3-4) ◽  
pp. 285-296
Author(s):  
Sanjay Swaminathan ◽  
Chantelle L. Hood ◽  
Kazuo Suzuki ◽  
Anthony D. Kelleher
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Gene Silencing ◽  
Gene Activation ◽  
Current Status ◽  
Transcriptional Gene Silencing ◽  
Regulatory Pathways ◽  
Rna Molecules ◽  
Post Transcriptional Gene Silencing ◽  
Rna Duplexes

AbstractTranscriptional regulation by small RNA molecules, including small interfering RNA and microRNA, has emerged as an important gene expression modulator. The regulatory pathways controlling gene expression, post-transcriptional gene silencing and transcriptional gene silencing (TGS) have been demonstrated in yeast, plants and more recently in human cells. In this review, we discuss the currents models of transcriptional regulation and the main components of the RNA-induced silencing complex and RNA-induced transcriptional silencing complex machinery, as well as confounding off-target effects and gene activation. We also discuss RNA-mediated TGS within the NF-κB motif of the human immunodeficiency virus type 1 5′ long tandem repeat promoter region and the associated epigenetic modifications. Finally, we outline the current RNA interference (RNAi) delivery methods and describe the current status of human trials investigating potential RNAi therapeutics for several human diseases.

scholarly journals Targets and Mechanisms of Geminivirus Silencing Suppressor Protein AC2

2021 ◽  
Vol 12 ◽  
Author(s):  
Karuppannan Veluthambi ◽  
Sukumaran Sunitha
Keyword(s):  
Gene Silencing ◽  
Defense Mechanism ◽  
Transcriptional Gene Silencing ◽  
Silencing Suppressor ◽  
Biotechnological Applications ◽  
Important Food ◽  
Dna Viruses ◽  
Post Transcriptional Gene Silencing ◽  
Transcriptional Activator Protein ◽  
Wide Range

Geminiviruses are plant DNA viruses that infect a wide range of plant species and cause significant losses to economically important food and fiber crops. The single-stranded geminiviral genome encodes a small number of proteins which act in an orchestrated manner to infect the host. The fewer proteins encoded by the virus are multifunctional, a mechanism uniquely evolved by the viruses to balance the genome-constraint. The host-mediated resistance against incoming virus includes post-transcriptional gene silencing, transcriptional gene silencing, and expression of defense responsive genes and other cellular regulatory genes. The pathogenicity property of a geminiviral protein is linked to its ability to suppress the host-mediated defense mechanism. This review discusses what is currently known about the targets and mechanism of the viral suppressor AC2/AL2/transcriptional activator protein (TrAP) and explore the biotechnological applications of AC2.

scholarly journals In plants, decapping prevents RDR6-dependent production of small interfering RNAs from endogenous mRNAs

2015 ◽  
Author(s):  
Angel Emilio Martínez de Alba ◽  
Ana Moreno ◽  
Marc Gabriel ◽  
Allison C Mallory ◽  
Aurélie Christ ◽  
...  
Keyword(s):  
Quality Control ◽  
Rna Polymerase ◽  
Gene Silencing ◽  
Transcriptional Gene Silencing ◽  
Small Interfering Rnas ◽  
Rna Dependent Rna Polymerase ◽  
P Bodies ◽  
New Class ◽  
Post Transcriptional Gene Silencing ◽  
Rna Quality Control

Cytoplasmic degradation of endogenous RNAs is an integral part of RNA quality control (RQC) and often relies on the removal of the 5’ cap structure and their subsequent 5’ to 3’ degradation in cytoplasmic processing (P-)bodies. In parallel, many eukaryotes degrade exogenous and selected endogenous RNAs through post-transcriptional gene silencing (PTGS). In plants, PTGS depends on small interfering (si)RNAs produced after the conversion of single-stranded RNAs to doublestranded RNAs by the cellular RNA DEPENDENT RNA POLYMERASE 6 (RDR6) in cytoplasmic siRNA-bodies. PTGS and RQC compete for transgene-derived RNAs, but it is unknown whether this competition also occurs for endogenous transcripts. We show that the lethality of decapping mutants is suppressed by impairing RDR6 activity. We establish that upon decapping impairment hundreds of endogenous mRNAs give rise to a new class of rqc-siRNAs, that over-accumulate when RQC processes are impaired, a subset of which depending on RDR6 for their production. We observe that P- and siRNA-bodies often are dynamically juxtaposed, potentially allowing for crosstalk of the two machineries. Our results suggest that the decapping of endogenous RNA limits their entry into the PTGS pathway. We anticipate that the rqc-siRNAs identified in decapping mutants represent a subset of a larger ensemble of endogenous siRNAs.

Host-induced gene silencing and spray-induced gene silencing for crop protection against viruses.

2021 ◽  
pp. 72-85
Author(s):  
Angela Ricci ◽  
Silvia Sabbadini ◽  
Laura Miozzi ◽  
Bruno Mezzetti ◽  
Emanuela Noris
Keyword(s):  
Gene Silencing ◽  
Plant Pathogens ◽  
Crop Protection ◽  
Plant Defence ◽  
Transcriptional Gene Silencing ◽  
Target Sequence ◽  
Sequence Specificity ◽  
Rna Molecules ◽  
Political Concern ◽  
Post Transcriptional Gene Silencing

Abstract Since the beginning of agriculture, plant virus diseases have been a strong challenge for farming. Following its discovery at the very beginning of the 1990s, the RNA interference (RNAi) mechanism has been widely studied and exploited as an integrative tool to obtain resistance to viruses in several plant species, with high target-sequence specificity. In this chapter, we describe and review the major aspects of host-induced gene silencing (HIGS), as one of the possible plant defence methods, using genetic engineering techniques. In particular, we focus our attention on the use of RNAi-based gene constructs to introduce stable resistance in host plants against viral diseases, by triggering post-transcriptional gene silencing (PTGS). Recently, spray-induced gene silencing (SIGS), consisting of the topical application of small RNA molecules to plants, has been explored as an alternative tool to the stable integration of RNAi-based gene constructs in plants. SIGS has great and innovative potential for crop defence against different plant pathogens and pests and is expected to raise less public and political concern, as it does not alter the genetic structure of the plant.

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