Special Issue "RNA Interference"

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A special issue of Genes (ISSN 2073-4425).

Deadline for manuscript submissions: closed (31 August 2012)

Special Issue Editor

Guest Editor
Prof. Dr. Jeremy C. Simpson (Website)

University College Dublin, School of Biology and Environmental Science, Science Center - West, Belfield, Dublin 4, Ireland
Phone: +353 1 716 2345
Interests: organisation and regulation of eukaryotic membrane traffic pathways

Special Issue Information

Dear Colleagues,

In the last ten years fewer techniques can have revolutionised life science research more than the ability to carry out gene downregulation studies in cultured cells in a straightforward and robust manner. The technique of RNA interference is now routinely applied in the study of probably all cellular processes and events. Furthermore, its ease of use and accessibility has resulted in it now being a mainstream tool in high-throughput functional genomics approaches to systematically study gene function. Perhaps also equally exciting is the use of RNAi in a therapeutic context, and efforts to improve the delivery of RNAi molecules to specific tissues and cells in vivo is now well advanced.

This special issue serves to highlight the importance of this technique in the life sciences. We are particularly keen to hear of new advances in the use of RNAi in cellular assays to understand gene function, however research or review articles on any topic within the RNAi field will be considered. We look forward to your contributions.

Prof. Dr. Jeremy C. Simpson
Guest Editor

Keywords

  • RNAi
  • siRNA
  • shRNA
  • gene downregulation
  • functional genomics
  • cellular assays
  • RNA therapeutics

Published Papers (9 papers)

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Research

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Open AccessArticle The Influence of Competition Among C. elegans Small RNA Pathways on Development
Genes 2012, 3(4), 671-685; doi:10.3390/genes3040671
Received: 17 August 2012 / Revised: 28 September 2012 / Accepted: 15 October 2012 / Published: 19 October 2012
Cited by 4 | PDF Full-text (881 KB) | HTML Full-text | XML Full-text
Abstract
Small RNAs play a variety of regulatory roles, including highly conserved developmental functions. Caenorhabditis elegans not only possesses most known small RNA pathways, it is also an easy system to study their roles and interactions during development. It has been proposed that [...] Read more.
Small RNAs play a variety of regulatory roles, including highly conserved developmental functions. Caenorhabditis elegans not only possesses most known small RNA pathways, it is also an easy system to study their roles and interactions during development. It has been proposed that in C. elegans, some small RNA pathways compete for access to common limiting resources. The strongest evidence supporting this model is that disrupting the production or stability of endogenous short interfering RNAs (endo-siRNAs) enhances sensitivity to experimentally induced exogenous RNA interference (exo-RNAi). Here, we examine the relationship between the endo-siRNA and microRNA (miRNA) pathways, and find that, consistent with competition among these endogenous small RNA pathways, endo-siRNA pathway mutants may enhance miRNA efficacy. Furthermore, we show that exo-RNAi may also compete with both endo-siRNAs and miRNAs. Our data thus provide support that all known Dicer-dependent small RNA pathways may compete for limiting common resources. Finally, we observed that both endo-siRNA mutants and animals experiencing exo-RNAi have increased expression of miRNA-regulated stage-specific developmental genes. These observations suggest that perturbing the small RNA flux and/or the induction of exo-RNAi, even in wild-type animals, may impact development via effects on the endo-RNAi and microRNA pathways. Full article
(This article belongs to the Special Issue RNA Interference)
Open AccessArticle Regulation of Fibroblast Growth Factor-2 Expression and Cell Cycle Progression by an Endogenous Antisense RNA
Genes 2012, 3(3), 505-520; doi:10.3390/genes3030505
Received: 27 June 2012 / Revised: 31 July 2012 / Accepted: 15 August 2012 / Published: 16 August 2012
Cited by 2 | PDF Full-text (684 KB) | HTML Full-text | XML Full-text
Abstract
Basic fibroblast growth factor (FGF2) is a potent wide-spectrum mitogen whose overexpression is associated with immortalization and unregulated cell proliferation in many tumors. The FGF2 gene locus is bi-directionally transcribed to produce FGF2 mRNA from the “sense” strand and a cis-antisense [...] Read more.
Basic fibroblast growth factor (FGF2) is a potent wide-spectrum mitogen whose overexpression is associated with immortalization and unregulated cell proliferation in many tumors. The FGF2 gene locus is bi-directionally transcribed to produce FGF2 mRNA from the “sense” strand and a cis-antisense RNA (NUDT6) from the NUDT6 gene on the “antisense” strand. The NUDT6 gene encodes a nudix motif protein of unknown function, while its mRNA has been implicated in the post-transcriptional regulation of FGF2 expression. FGF2 and NUDT6 are co-expressed in rat C6 glioma cells, and ectopic overexpression of NUDT6 suppresses cellular FGF2 accumulation and cell cycle progression. However, the role of the endogenous antisense RNA in regulation of FGF2 is unclear. In the present study, we employed siRNA-mediated gene knockdown to examine the role of the endogenous NUDT6 RNA in regulation of FGF2 expression and cell cycle progression. Knockdown of either FGF2 or NUDT6 mRNA was accompanied by a significant (>3 fold) increase in the complementary partner RNA. Similar reciprocal effects were observed at the protein level, indicating that these two transcripts are mutually regulatory. Remarkably, knockdown of either FGF2 or NUDT6 significantly reduced cell proliferation and inhibited S-phase re-entry following serum deprivation, implicating both FGF2 and NUDT6 in the regulation of cell transformation and cell cycle progression. Full article
(This article belongs to the Special Issue RNA Interference)
Figures

Open AccessArticle siRNAs Trigger Efficient Silencing of a Parasitism Gene in Plant Parasitic Root-Knot Nematodes
Genes 2012, 3(3), 391-408; doi:10.3390/genes3030391
Received: 10 May 2012 / Revised: 18 June 2012 / Accepted: 26 June 2012 / Published: 10 July 2012
Cited by 5 | PDF Full-text (240 KB) | HTML Full-text | XML Full-text
Abstract
Expanding genomic data on plant pathogens open new perspectives for the development of specific and environment friendly pest management strategies based on the inhibition of parasitism genes that are essential for the success of infection. Identifying such genes relies on accurate reverse [...] Read more.
Expanding genomic data on plant pathogens open new perspectives for the development of specific and environment friendly pest management strategies based on the inhibition of parasitism genes that are essential for the success of infection. Identifying such genes relies on accurate reverse genetics tools and the screening of pathogen knock-down phenotypes. Root-knot nematodes are major cosmopolitan crop pests that feed on a wide range of host plants. Small interfering RNAs (siRNAs) would provide a powerful tool for reverse genetics of nematode parasitism genes provided that they could (1) target genes expressed in inner tissues of infective nematodes and (2) target genes expressed during parasitism. In this study, we show that siRNAs can access inner tissues of the infective juveniles during soaking and accumulate in the esophagus, amphidial pouches and related neurons of the nematode. We provide evidence that siRNAs can trigger knock-down of the parasitism gene Mi-CRT, a calreticulin gene expressed in the esophageal glands of Meloidogyne incognita. Mi-CRT knock-down in infective juveniles affected nematode virulence. However, Mi-CRT knock-down was not persistent after plant infection, indicating that siRNA-mediated RNAi is best suited for functional analysis of genes involved in pre-parasitic stages or in the early steps of infection. Full article
(This article belongs to the Special Issue RNA Interference)
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Review

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Open AccessReview MicroRNAs and Molecular Mechanisms of Neurodegeneration
Genes 2013, 4(2), 244-263; doi:10.3390/genes4020244
Received: 29 March 2013 / Revised: 9 May 2013 / Accepted: 10 May 2013 / Published: 29 May 2013
Cited by 9 | PDF Full-text (454 KB) | HTML Full-text | XML Full-text
Abstract
During the last few years microRNAs (miRNAs) have emerged as key mediators of post-transcriptional and epigenetic regulation of gene expression. MiRNAs targets, identified through gene expression profiling and studies in animal models, depict a scenario where miRNAs are fine-tuning metabolic pathways and [...] Read more.
During the last few years microRNAs (miRNAs) have emerged as key mediators of post-transcriptional and epigenetic regulation of gene expression. MiRNAs targets, identified through gene expression profiling and studies in animal models, depict a scenario where miRNAs are fine-tuning metabolic pathways and genetic networks in both plants and animals. MiRNAs have shown to be differentially expressed in brain areas and alterations of miRNAs homeostasis have been recently correlated to pathological conditions of the nervous system, such as cancer and neurodegeneration. Here, we review and discuss the most recent insights into the involvement of miRNAs in the neurodegenerative mechanisms and their correlation with significant neurodegenerative disorders. Full article
(This article belongs to the Special Issue RNA Interference)
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Open AccessReview The Sound of Silence: RNAi in Poly (ADP-Ribose) Research
Genes 2012, 3(4), 779-805; doi:10.3390/genes3040779
Received: 4 September 2012 / Revised: 5 November 2012 / Accepted: 6 November 2012 / Published: 6 December 2012
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Abstract
Poly(ADP-ribosyl)-ation is a nonprotein posttranslational modification of proteins and plays an integral part in cell physiology and pathology. The metabolism of poly(ADP-ribose) (PAR) is regulated by its synthesis by poly(ADP-ribose) polymerases (PARPs) and on the catabolic side by poly(ADP-ribose) glycohydrolase (PARG). PARPs [...] Read more.
Poly(ADP-ribosyl)-ation is a nonprotein posttranslational modification of proteins and plays an integral part in cell physiology and pathology. The metabolism of poly(ADP-ribose) (PAR) is regulated by its synthesis by poly(ADP-ribose) polymerases (PARPs) and on the catabolic side by poly(ADP-ribose) glycohydrolase (PARG). PARPs convert NAD+ molecules into PAR chains that interact covalently or noncovalently with target proteins and thereby modify their structure and functions. PAR synthesis is activated when PARP1 and PARP2 bind to DNA breaks and these two enzymes account for almost all PAR formation after genotoxic stress. PARG cleaves PAR molecules into free PAR and finally ADP-ribose (ADPR) moieties, both acting as messengers in cellular stress signaling. In this review, we discuss the potential of RNAi to manipulate the levels of PARPs and PARG, and consequently those of PAR and ADPR, and compare the results with those obtained after genetic or chemical disruption. Full article
(This article belongs to the Special Issue RNA Interference)
Open AccessReview Use of RNA Interference by In Utero Electroporation to Study Cortical Development: The Example of the Doublecortin Superfamily
Genes 2012, 3(4), 759-778; doi:10.3390/genes3040759
Received: 27 September 2012 / Revised: 22 October 2012 / Accepted: 31 October 2012 / Published: 21 November 2012
Cited by 1 | PDF Full-text (645 KB) | HTML Full-text | XML Full-text
Abstract
The way we study cortical development has undergone a revolution in the last few years following the ability to use shRNA in the developing brain of the rodent embryo. The first gene to be knocked-down in the developing brain was doublecortin (Dcx). [...] Read more.
The way we study cortical development has undergone a revolution in the last few years following the ability to use shRNA in the developing brain of the rodent embryo. The first gene to be knocked-down in the developing brain was doublecortin (Dcx). Here we will review knockdown experiments in the developing brain and compare them with knockout experiments, thus highlighting the advantages and disadvantages using the different systems. Our review will focus on experiments relating to the doublecortin superfamily of proteins. Full article
(This article belongs to the Special Issue RNA Interference)
Open AccessReview RNAi in Arthropods: Insight into the Machinery and Applications for Understanding the Pathogen-Vector Interface
Genes 2012, 3(4), 702-741; doi:10.3390/genes3040702
Received: 3 September 2012 / Revised: 19 October 2012 / Accepted: 23 October 2012 / Published: 6 November 2012
Cited by 6 | PDF Full-text (686 KB) | HTML Full-text | XML Full-text
Abstract
The availability of genome sequencing data in combination with knowledge of expressed genes via transcriptome and proteome data has greatly advanced our understanding of arthropod vectors of disease. Not only have we gained insight into vector biology, but also into their respective [...] Read more.
The availability of genome sequencing data in combination with knowledge of expressed genes via transcriptome and proteome data has greatly advanced our understanding of arthropod vectors of disease. Not only have we gained insight into vector biology, but also into their respective vector-pathogen interactions. By combining the strengths of postgenomic databases and reverse genetic approaches such as RNAi, the numbers of available drug and vaccine targets, as well as number of transgenes for subsequent transgenic or paratransgenic approaches, have expanded. These are now paving the way for in-field control strategies of vectors and their pathogens. Basic scientific questions, such as understanding the basic components of the vector RNAi machinery, is vital, as this allows for the transfer of basic RNAi machinery components into RNAi-deficient vectors, thereby expanding the genetic toolbox of these RNAi-deficient vectors and pathogens. In this review, we focus on the current knowledge of arthropod vector RNAi machinery and the impact of RNAi on understanding vector biology and vector-pathogen interactions for which vector genomic data is available on VectorBase. Full article
(This article belongs to the Special Issue RNA Interference)
Open AccessReview Using Multiple Phenotype Assays and Epistasis Testing to Enhance the Reliability of RNAi Screening and Identify Regulators of Muscle Protein Degradation
Genes 2012, 3(4), 686-701; doi:10.3390/genes3040686
Received: 13 August 2012 / Revised: 27 September 2012 / Accepted: 30 October 2012 / Published: 2 November 2012
Cited by 4 | PDF Full-text (416 KB) | HTML Full-text | XML Full-text
Abstract
RNAi is a convenient, widely used tool for screening for genes of interest. We have recently used this technology to screen roughly 750 candidate genes, in C. elegans, for potential roles in regulating muscle protein degradation in vivo. To maximize [...] Read more.
RNAi is a convenient, widely used tool for screening for genes of interest. We have recently used this technology to screen roughly 750 candidate genes, in C. elegans, for potential roles in regulating muscle protein degradation in vivo. To maximize confidence and assess reproducibility, we have only used previously validated RNAi constructs and have included time courses and replicates. To maximize mechanistic understanding, we have examined multiple sub-cellular phenotypes in multiple compartments in muscle. We have also tested knockdowns of putative regulators of degradation in the context of mutations or drugs that were previously shown to inhibit protein degradation by diverse mechanisms. Here we discuss how assaying multiple phenotypes, multiplexing RNAi screens with use of mutations and drugs, and use of bioinformatics can provide more data on rates of potential false positives and negatives as well as more mechanistic insight than simple RNAi screening. Full article
(This article belongs to the Special Issue RNA Interference)
Open AccessReview Hints of tRNA-Derived Small RNAs Role in RNA Silencing Mechanisms
Genes 2012, 3(4), 603-614; doi:10.3390/genes3040603
Received: 24 August 2012 / Revised: 26 September 2012 / Accepted: 28 September 2012 / Published: 10 October 2012
Cited by 14 | PDF Full-text (400 KB) | HTML Full-text | XML Full-text
Abstract
With the advent of new and improved high-throughput sequencing technologies in the last few years, a growing number of novel classes of small RNA, other than miRNAs or siRNA, has emerged, which appear as new actors in gene expression regulation. tRNA-derived small [...] Read more.
With the advent of new and improved high-throughput sequencing technologies in the last few years, a growing number of novel classes of small RNA, other than miRNAs or siRNA, has emerged, which appear as new actors in gene expression regulation. tRNA-derived small RNAs represent one of these novel members that are, surprisingly, among the most conserved class of small RNAs throughout evolution. They could represent the most primitive small RNA pathways from which the well-known canonical RNA silencing pathways reported in higher eukaryotes evolved. This review aims to make a compilation of the most relevant research literature in this field with the purpose of shedding light on the relation of these primitive tRNA-derived molecules with the gene silencing machinery. Full article
(This article belongs to the Special Issue RNA Interference)

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