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RNA Interference
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RNA Interference

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (29 April 2015) | Viewed by 86046

Special Issue Editor

Dr. Michael R. Ladomery

E-Mail Website
Guest Editor
Faculty of Health and Applied Sciences, University of the West of England, Bristol BS16 1QY, UK
Interests: RNA biology; RNA binding proteins; alternative splicing; splice factors; splice factor kinases; mRNA translation; microRNAs
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleague,

In 2006, Craig Fire and Andrew Mello shared a Nobel Prize in Physiology or Medicine for their pioneering work on the nematode Caenorhabditis elegans that led to the discovery of RNA interference. Other groups, working on plants, fruit flies and other organisms also contributed, causing huge excitement in the field because it became obvious that small noncoding RNAs play important roles in gene regulation. These noncoding RNAs include siRNAs (small interfering RNAs derived from dsRNA precursors through cleaved by Dicer) and microRNAs (transcribed from endogenous genes and processed in the nucleus). They bind to target mRNAs, typically the 3'UTR, causing the translational repression or even active degradation of target mRNAs. RNA interference is an ancient process thought to have evolved in order to defend cells against the havoc caused by viruses, parasites and transposons. MicroRNA research has boomed impressively; it is very clear that these noncoding RNAs have critically important developmental roles. The misexpression of microRNAs is associated with several important diseases including cancer, diabetes, and neurodegenerative disorders amongst many others. The ability to detect microRNAs in the blood provides further opportunities for diagnostic testing. RNA interference technology has provided outstanding opportunities in functional genomics, and potentially even novel therapeutic strategies. The purpose of this Special Issue is to highlight recent, exciting advances in RNA interference research. We want to highlight significant applications of RNA interference in biomedical science, agriculture and other areas. In doing so, we plan to underline both the enormous potential and significant practical difficulties in implementing this technology. We also invite articles on the latest developments in terms of understanding the molecular mechanisms that underpin RNA interference: for example, how is the expression of the complex machinery of RNA interference regulated? And how do siRNAs and microRNAs find their correct targets in vivo?

Dr. Michael R. Ladomery
Guest Editor

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Keywords

  • RNA interference
  • short noncoding RNAs
  • siRNAs
  • shRNAs
  • microRNAs
  • RISC complex

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Published Papers (9 papers)

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Research

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2730 KiB  
Article
Human Papillomavirus E6/E7-Specific siRNA Potentiates the Effect of Radiotherapy for Cervical Cancer in Vitro and in Vivo
by Hun Soon Jung, Nirmal Rajasekaran, Sang Yong Song, Young Deug Kim, Sungyoul Hong, Hyuck Jae Choi, Young Seok Kim, Jong-Sun Choi, Yoon-La Choi and Young Kee Shin
Int. J. Mol. Sci. 2015, 16(6), 12243-12260; https://doi.org/10.3390/ijms160612243 - 29 May 2015
Cited by 19 | Viewed by 9174
Abstract
The functional inactivation of TP53 and Rb tumor suppressor proteins by the HPV-derived E6 and E7 oncoproteins is likely an important step in cervical carcinogenesis. We have previously shown siRNA technology to selectively silence both E6/E7 oncogenes and demonstrated that the [...] Read more.
The functional inactivation of TP53 and Rb tumor suppressor proteins by the HPV-derived E6 and E7 oncoproteins is likely an important step in cervical carcinogenesis. We have previously shown siRNA technology to selectively silence both E6/E7 oncogenes and demonstrated that the synthetic siRNAs could specifically block its expression in HPV-positive cervical cancer cells. Herein, we investigated the potentiality of E6/E7 siRNA candidates as radiosensitizers of radiotherapy for the human cervical carcinomas. HeLa and SiHa cells were transfected with HPV E6/E7 siRNA; the combined cytotoxic effect of E6/E7 siRNA and radiation was assessed by using the cell viability assay, flow cytometric analysis and the senescence-associated β-galactosidase (SA-β-Gal) assay. In addition, we also investigated the effect of combined therapy with irradiation and E6/E7 siRNA intravenous injection in an in vivo xenograft model. Combination therapy with siRNA and irradiation efficiently retarded tumor growth in established tumors of human cervical cancer cell xenografted mice. In addition, the chemically-modified HPV16 and 18 E6/E7 pooled siRNA in combination with irradiation strongly inhibited the growth of cervical cancer cells. Our results indicated that simultaneous inhibition of HPV E6/E7 oncogene expression with radiotherapy can promote potent antitumor activity and radiosensitizing activity in human cervical carcinomas. Full article
(This article belongs to the Special Issue RNA Interference)
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2427 KiB  
Article
Sequence Features of Drosha and Dicer Cleavage Sites Affect the Complexity of IsomiRs
by Julia Starega-Roslan, Tomasz M. Witkos, Paulina Galka-Marciniak and Wlodzimierz J. Krzyzosiak
Int. J. Mol. Sci. 2015, 16(4), 8110-8127; https://doi.org/10.3390/ijms16048110 - 10 Apr 2015
Cited by 41 | Viewed by 9348
Abstract
The deep-sequencing of small RNAs has revealed that different numbers and proportions of miRNA variants called isomiRs are formed from single miRNA genes and that this effect is attributable mainly to imprecise cleavage by Drosha and Dicer. Factors that influence the degree of [...] Read more.
The deep-sequencing of small RNAs has revealed that different numbers and proportions of miRNA variants called isomiRs are formed from single miRNA genes and that this effect is attributable mainly to imprecise cleavage by Drosha and Dicer. Factors that influence the degree of cleavage precision of Drosha and Dicer are under investigation, and their identification may improve our understanding of the mechanisms by which cells modulate the regulatory potential of miRNAs. In this study, we focused on the sequences and structural determinants of Drosha and Dicer cleavage sites, which may explain the generation of homogeneous miRNAs (in which a single isomiR strongly predominates) as well as the generation of heterogeneous miRNAs. Using deep-sequencing data for small RNAs, we demonstrate that the generation of homogeneous miRNAs requires more sequence constraints at the cleavage sites than the formation of heterogeneous miRNAs. Additionally, our results indicate that specific Drosha cleavage sites have more sequence determinants in miRNA precursors than specific cleavage sites for Dicer and that secondary structural motifs in the miRNA precursors influence the precision of Dicer cleavage. Together, we present the sequence and structural features of Drosha and Dicer cleavage sites that influence the heterogeneity of the released miRNAs. Full article
(This article belongs to the Special Issue RNA Interference)
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4283 KiB  
Article
MiR-222 Targeted PUMA to Improve Sensitization of UM1 Cells to Cisplatin
by Fangfang Jiang, Wei Zhao, Lijie Zhou, Zifeng Liu, Wenqing Li and Dongsheng Yu
Int. J. Mol. Sci. 2014, 15(12), 22128-22141; https://doi.org/10.3390/ijms151222128 - 2 Dec 2014
Cited by 27 | Viewed by 5804
Abstract
microRNAs have been shown to play critical roles in regulating the chemosensitivity of cancer cells. As a member of the oncogenic miRNAs (oncomiRs), miR-222 has been reported to drive the oncogenesis of many types of malignancies. However, little is known concerning the specific [...] Read more.
microRNAs have been shown to play critical roles in regulating the chemosensitivity of cancer cells. As a member of the oncogenic miRNAs (oncomiRs), miR-222 has been reported to drive the oncogenesis of many types of malignancies. However, little is known concerning the specific role of miR-222 in human oral squamous cell carcinoma (OSCC). The present study explored the role and mechanism of miR-222 in increasing the expression of p53 up-regulated modulator of apoptosis (PUMA) and enhancing the sensitivity of OSCC to cisplatin (CDDP). Results showed that antisense (As)-miR-222 inhibits the expression of miR-222. In contrast, PUMA was dramaticallyup-regulated. IC50 values were significantly decreased in cells treated with As-miR-222 combined with CDDP, to a greater extent than in cells treated with CDDP alone. Furthermore, As-miR-222 enhanced apoptosis and inhibited the invasiveness of UM1 cells. Analysis of the above data suggested that, in UM1 cells, there might be a regulatory loop between miR-222 and PUMA, and that miR-222 inhibition increased the chemosensitivity to CDDP. These findings demonstrated that down-regulation of miR-222 could enhance the chemosensitivity of human OSCC cells to CDDP, and that the combination of As-miR-222 and CDDP could be an effective therapeutic strategy by boosting the expression of PUMA for controlling the growth of OSCC. Full article
(This article belongs to the Special Issue RNA Interference)
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2122 KiB  
Article
Se-Methylselenocysteine Inhibits Apoptosis Induced by Clusterin Knockdown in Neuroblastoma N2a and SH-SY5Y Cell Lines
by Chao Wang, Zhenyu Zeng, Qiong Liu, Renli Zhang and Jiazuan Ni
Int. J. Mol. Sci. 2014, 15(11), 21331-21347; https://doi.org/10.3390/ijms151121331 - 18 Nov 2014
Cited by 5 | Viewed by 7446
Abstract
Apoptosis, as a programmed cell death process, is essential for the maintenance of tissue function in organisms. Alteration of this process is linked to many diseases. Over-expression of clusterin (Clu) can antagonize apoptosis in various cells. Selenium (Se) is an essential trace element [...] Read more.
Apoptosis, as a programmed cell death process, is essential for the maintenance of tissue function in organisms. Alteration of this process is linked to many diseases. Over-expression of clusterin (Clu) can antagonize apoptosis in various cells. Selenium (Se) is an essential trace element for human health. Its biological function is also associated with cell apoptosis. To explore the function of Clu and the impact of Se in the process of apoptosis, several short-hairpin RNAs (shRNA) were designed for the construction of two sets of recombinant plasmids: one set for plasmid-transfection of mouse neuroblastoma N2a cells (N2a cells); and the other set for lentiviral infection of human neuroblastoma SH-SY5Y cells (SH-SY5Y cells). These shRNAs specifically and efficiently interfered with the intracellular expression of Clu at both the mRNA and protein levels. The Clu-knockdown cells showed apoptosis-related features, including down-regulation of antioxidative capacity and the Bcl-2/Bax ratio and up-regulation of caspase-8 activity. Se-methylselenocysteine (MSC) at an optimum concentration of 1 μM could reverse the alteration in antioxidative capacity, Bcl2/Bax ratio and caspase-8 activity caused by Clu-knockdown, thus inhibiting apoptosis and maintaining cell viability. The results hereby imply the potentiality of Clu and Se in neuroprotection. Full article
(This article belongs to the Special Issue RNA Interference)
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Review

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395 KiB  
Review
RNA Interference in the Age of CRISPR: Will CRISPR Interfere with RNAi?
by Unnikrishnan Unniyampurath, Rajendra Pilankatta and Manoj N. Krishnan
Int. J. Mol. Sci. 2016, 17(3), 291; https://doi.org/10.3390/ijms17030291 - 26 Feb 2016
Cited by 63 | Viewed by 12165
Abstract
The recent emergence of multiple technologies for modifying gene structure has revolutionized mammalian biomedical research and enhanced the promises of gene therapy. Over the past decade, RNA interference (RNAi) based technologies widely dominated various research applications involving experimental modulation of gene expression at [...] Read more.
The recent emergence of multiple technologies for modifying gene structure has revolutionized mammalian biomedical research and enhanced the promises of gene therapy. Over the past decade, RNA interference (RNAi) based technologies widely dominated various research applications involving experimental modulation of gene expression at the post-transcriptional level. Recently, a new gene editing technology, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and the CRISPR-associated protein 9 (Cas9) (CRISPR/Cas9) system, has received unprecedented acceptance in the scientific community for a variety of genetic applications. Unlike RNAi, the CRISPR/Cas9 system is bestowed with the ability to introduce heritable precision insertions and deletions in the eukaryotic genome. The combination of popularity and superior capabilities of CRISPR/Cas9 system raises the possibility that this technology may occupy the roles currently served by RNAi and may even make RNAi obsolete. We performed a comparative analysis of the technical aspects and applications of the CRISPR/Cas9 system and RNAi in mammalian systems, with the purpose of charting out a predictive picture on whether the CRISPR/Cas9 system will eclipse the existence and future of RNAi. The conclusion drawn from this analysis is that RNAi will still occupy specific domains of biomedical research and clinical applications, under the current state of development of these technologies. However, further improvements in CRISPR/Cas9 based technology may ultimately enable it to dominate RNAi in the long term. Full article
(This article belongs to the Special Issue RNA Interference)
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929 KiB  
Review
The miR-200 Family: Versatile Players in Epithelial Ovarian Cancer
by Goda G. Muralidhar and Maria V. Barbolina
Int. J. Mol. Sci. 2015, 16(8), 16833-16847; https://doi.org/10.3390/ijms160816833 - 24 Jul 2015
Cited by 65 | Viewed by 8455
Abstract
The role of microRNAs (miRNAs or miRs) in the pathology of epithelial ovarian cancer (EOC) has been extensively studied. Many miRNAs differentially expressed in EOC as compared to normal controls have been identified, prompting further inquiry into their role in the disease. miRNAs [...] Read more.
The role of microRNAs (miRNAs or miRs) in the pathology of epithelial ovarian cancer (EOC) has been extensively studied. Many miRNAs differentially expressed in EOC as compared to normal controls have been identified, prompting further inquiry into their role in the disease. miRNAs belonging to the miR-200 family have repeatedly surfaced over multiple profiling studies. In this review, we attempt to consolidate the data from different studies and highlight mechanisms by which these miRNAs influence progression of metastasis and chemo-resistance in EOC. Full article
(This article belongs to the Special Issue RNA Interference)
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1962 KiB  
Review
Conformational Dynamics of Ago-Mediated Silencing Processes
by Sarah Willkomm and Tobias Restle
Int. J. Mol. Sci. 2015, 16(7), 14769-14785; https://doi.org/10.3390/ijms160714769 - 1 Jul 2015
Cited by 13 | Viewed by 5976
Abstract
Argonaute (Ago) proteins are key players of nucleic acid-based interference mechanisms. Their domains and structural organization are widely conserved in all three domains of life. However, different Ago proteins display various substrate preferences. While some Ago proteins are able to use several substrates, [...] Read more.
Argonaute (Ago) proteins are key players of nucleic acid-based interference mechanisms. Their domains and structural organization are widely conserved in all three domains of life. However, different Ago proteins display various substrate preferences. While some Ago proteins are able to use several substrates, others are limited to a single one. Thereby, they were demonstrated to act specifically on their preferred substrates. Here, we discuss mechanisms of Ago-mediated silencing in relation to structural and biochemical insights. The combination of biochemical and structural information enables detailed analyses of the complex dynamic interplay between Ago proteins and their substrates. Especially, transient binding data allow precise investigations of structural transitions taking place upon Ago-mediated guide and target binding. Full article
(This article belongs to the Special Issue RNA Interference)
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2054 KiB  
Review
Small RNA Detection by in Situ Hybridization Methods
by Martyna O. Urbanek, Anna U. Nawrocka and Wlodzimierz J. Krzyzosiak
Int. J. Mol. Sci. 2015, 16(6), 13259-13286; https://doi.org/10.3390/ijms160613259 - 10 Jun 2015
Cited by 79 | Viewed by 17201
Abstract
Small noncoding RNAs perform multiple regulatory functions in cells, and their exogenous mimics are widely used in research and experimental therapies to interfere with target gene expression. MicroRNAs (miRNAs) are the most thoroughly investigated representatives of the small RNA family, which includes short [...] Read more.
Small noncoding RNAs perform multiple regulatory functions in cells, and their exogenous mimics are widely used in research and experimental therapies to interfere with target gene expression. MicroRNAs (miRNAs) are the most thoroughly investigated representatives of the small RNA family, which includes short interfering RNAs (siRNAs), PIWI-associated RNA (piRNAs), and others. Numerous methods have been adopted for the detection and characterization of small RNAs, which is challenging due to their short length and low level of expression. These include molecular biology methods such as real-time RT-PCR, northern blotting, hybridization to microarrays, cloning and sequencing, as well as single cell miRNA detection by microscopy with in situ hybridization (ISH). In this review, we focus on the ISH method, including its fluorescent version (FISH), and we present recent methodological advances that facilitated its successful adaptation for small RNA detection. We discuss relevant technical aspects as well as the advantages and limitations of ISH. We also refer to numerous applications of small RNA ISH in basic research and molecular diagnostics. Full article
(This article belongs to the Special Issue RNA Interference)
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956 KiB  
Review
Development of Small RNA Delivery Systems for Lung Cancer Therapy
by Yu Fujita, Kazuyoshi Kuwano and Takahiro Ochiya
Int. J. Mol. Sci. 2015, 16(3), 5254-5270; https://doi.org/10.3390/ijms16035254 - 6 Mar 2015
Cited by 52 | Viewed by 9514
Abstract
RNA interference (RNAi) has emerged as a powerful tool for studying target identification and holds promise for the development of therapeutic gene silencing. Recent advances in RNAi delivery and target selection provide remarkable opportunities for translational medical research. The induction of RNAi relies [...] Read more.
RNA interference (RNAi) has emerged as a powerful tool for studying target identification and holds promise for the development of therapeutic gene silencing. Recent advances in RNAi delivery and target selection provide remarkable opportunities for translational medical research. The induction of RNAi relies on small silencing RNAs, which affect specific messenger RNA (mRNA) degradation. Two types of small RNA molecules, small interfering RNAs (siRNAs) and microRNAs (miRNAs), have a central function in RNAi technology. The success of RNAi-based therapeutic delivery may be dependent upon uncovering a delivery route, sophisticated delivery carriers, and nucleic acid modifications. Lung cancer is still the leading cause of cancer death worldwide, for which novel therapeutic strategies are critically needed. Recently, we have reported a novel platform (PnkRNA™ and nkRNA®) to promote naked RNAi approaches through inhalation without delivery vehicles in lung cancer xenograft models. We suggest that a new class of RNAi therapeutic agent and local drug delivery system could also offer a promising RNAi-based strategy for clinical applications in cancer therapy. In this article, we show recent strategies for an RNAi delivery system and suggest the possible clinical usefulness of RNAi-based therapeutics for lung cancer treatment. Full article
(This article belongs to the Special Issue RNA Interference)
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