Regulation of Gene Expression by RNA-Mediated Transcriptional Gene Silencing

Selective regulation of gene expression by means of RNA interference has revolutionized molecular biology. This approach is not only used in fundamental studies on the roles of particular genes in the functioning of various organisms, but also possesses practical applications. A variety of methods are being developed based on gene silencing using dsRNA—for protecting agricultural plants from various pathogens, controlling insect reproduction, and therapeutic techniques related to the oncological disease treatment. One of the main problems in this research area is the successful delivery of exogenous dsRNA into cells, as this can be greatly affected by the localization or origin of tumor. This overview is dedicated to describing the latest advances in the development of various transport agents for the delivery of dsRNA fragments for gene silencing, with an emphasis on cancer treatment.

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What are natural antisense transcripts good for?

Biochemical Society Transactions ◽

10.1042/bst0381144 ◽

2010 ◽

Vol 38 (4) ◽

pp. 1144-1149 ◽

Cited By ~ 30

Author(s):

Andreas Werner ◽

Daniel Swan

Keyword(s):

Gene Expression ◽

Gene Silencing ◽

Higher Order ◽

Transcriptional Gene Silencing ◽

Antisense Transcripts ◽

Natural Antisense Transcripts ◽

Protein Coding ◽

Eukaryotic Gene Expression ◽

Eukaryotic Gene

NATs (natural antisense transcripts) are important regulators of eukaryotic gene expression. Interference between the expression of protein-coding sense transcripts and the corresponding NAT is well documented. In the present review, we focus on an additional, higher-order role of NATs that is currently emerging. The recent discovery of endogenous siRNAs (short interfering RNAs), as well as NAT-induced transcriptional gene silencing, are key to the proposed novel function of NATs.

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VEGF Specific siRNAs Act Synergistically with Bortezomib and Steroids in Inhibiting VEGF Gene Expression, Proliferation and Induction of Apoptosis in Multiple Myeloma Cells.

Blood ◽

10.1182/blood.v104.11.5266.5266 ◽

2004 ◽

Vol 104 (11) ◽

pp. 5266-5266

Author(s):

Michael Koldehoff ◽

Nina K. Steckel ◽

Rudolf Trenschel ◽

Dietrich W. Beelen ◽

Ahmet H. Elmaagacli

Keyword(s):

Gene Expression ◽

Multiple Myeloma ◽

Bone Marrow ◽

Gene Silencing ◽

Antitumor Agents ◽

Synergistic Effects ◽

Transcriptional Gene Silencing ◽

Vegf Gene ◽

Post Transcriptional Gene Silencing ◽

Induction Of Apoptosis

Abstract Multiple myeloma (MM) is a clonal B-cell malignancy characterized by the accumulation of malignant plasma cells within the bone marrow (BM). Vascular endothelial growth factor (VEGF), a glycoprotein produced by normal and neoplastic cells is an important regulator of physiological and pathological angiogenesis. MM cells secrete VEGF, which promotes production of cytokines in bone marrow stromal cells, as well as migration and proliferation of the tumor cells. Inhibition of VEGF activity or disabling the function of its receptors has been shown to inhibit both tumor growth and spread of metastases in a variety of animal tumor models. RNA interference (RNAi) is rapidly being established as a post-transcriptional gene silencing method and holds promise to specifically inhibit gene expression in mammals. Another novel class of antitumor agents is based on the inhibition of the ubiquitin-proteosomal system which represents the major nonlysosomal pathway through which intracellular proteins are degraded in eukaryotic cells. Bortezomib, a reversible proteosome inhibitor, shows remarkable anticancer activity in various malignant cell types, including MM cells that are resistant to conventional therapies. We studied the effect of transfection with small interfering RNA (siRNA) targeting VEGF in MM cells in terms of proliferation, induction of apoptosis, and cell differentiation. Further, we evaluated if the effects of post-transcriptional gene silencing by VEGF specific siRNA can be augmented by bortezomib and/or steroids in the cell line OPM-2. A mean reduction of VEGF gene expression to 38% as determined by real-time PCR was observed with 0.8 ug VEGF siRNA in OPM-2 cells compared to controls (controls were set up to 100%). Simultaneous administration of bortezomib and siRNA was able to reduce VEGF gene expression down to 23% compared to VEGF siRNA alone demonstrating a synergistic effect of combined bortezomib and siRNA treatment. We found a 2.5-fold increase in induced apoptosis in OPM-2 cells subsequent to VEGF siRNA administration but we saw no additional stimulation of apoptosis after combination of VEGF siRNA with bortezomib and/or steroids. Proliferation in OPM-2 cells was strongly inhibited (about 91%) following combination treatment as opposed to only 62% after administration of VEGF siRNA alone. The transfection of VEGF siRNA in OPM-2 cells had no influence on the expression levels of differentiation markers such as CD38, CD138, CD19, CD34, CD45, and CD7AAD. Our findings suggest that synergistic effects of VEGF siRNA with bortezomib and dexamethason may offer new therapeutic options in the treatment of MM.

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Therapeutic targeting of non-coding RNAs

Essays in Biochemistry ◽

10.1042/bse0540127 ◽

2013 ◽

Vol 54 ◽

pp. 127-145 ◽

Cited By ~ 34

Author(s):

Thomas C. Roberts ◽

Matthew J.A. Wood

Keyword(s):

Gene Expression ◽

Antisense Oligonucleotides ◽

Regulation Of Gene Expression ◽

Gene Activation ◽

Mature Mirnas ◽

Transcriptional Gene Silencing ◽

Small Interfering Rnas ◽

Promising Therapeutic Approach ◽

Non Coding Rnas ◽

Mirna Sponges

ncRNAs (non-coding RNAs) are implicated in a wide variety of cellular processes, including the regulation of gene expression. In the present chapter we consider two classes of ncRNA: miRNAs (microRNAs) which are post-transcriptional regulators of gene expression and lncRNAs (long ncRNAs) which mediate interactions between epigenetic remodelling complexes and chromatin. Mutation and misexpression of ncRNAs have been implicated in many disease conditions and, as such, pharmacological modulation of ncRNAs is a promising therapeutic approach. miRNA activity can be antagonized with antisense oligonucleotides which sequester or degrade mature miRNAs, and expressed miRNA sponges which compete with target transcripts for miRNA binding. Conversely, synthetic or expressed miRNA mimics can be used to treat a deficiency in miRNA expression. Similarly, conventional antisense technologies can be used to silence lncRNAs. Targeting promoter-associated RNAs with siRNAs (small interfering RNAs) results in recruitment of chromatin-modifying activities and induces transcriptional gene silencing. Alternatively, targeting natural antisense transcripts with siRNAs or antisense oligonucleotides can abrogate endogenous epigenetic silencing leading to transcriptional gene activation. The ability to modulate gene expression at the epigenetic level presents exciting new opportunities for the treatment of human disease.

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DDX21 interacts with nuclear AGO2 and regulates the alternative splicing of SMN2

Bioscience Biotechnology and Biochemistry ◽

10.1093/bbb/zbaa029 ◽

2020 ◽

Vol 85 (2) ◽

pp. 272-279

Author(s):

Mengting Gong ◽

Xi Zhang ◽

Yaru Wang ◽

Guiyan Mao ◽

Yangqi Ou ◽

...

Keyword(s):

Gene Expression ◽

Alternative Splicing ◽

Gene Silencing ◽

Target Gene ◽

Molecular Mechanisms ◽

Regulation Of Gene Expression ◽

Dependent Manner ◽

Indirect Interaction ◽

Multiple Gene ◽

Multiple Gene Silencing

ABSTRACT AGO2 is the only member of mammalian Ago protein family that possesses the catalytic activity and plays a central role in gene silencing. Recently researches reported that multiple gene silencing factors, including AGO2, function in the nuclei. The molecular mechanisms of the gene silencing factors functioning in nuclei are conducive to comprehend the roles of gene silencing in pretranslational regulation of gene expression. Here, we report that AGO2 interacts with DDX21 indirectly in an RNA-dependent manner by Co-IP and GST-Pulldown assays and the 2 proteins present nuclei foci in the immunofluorescence experiments. We found that DDX21 up-regulated the protein level of AGO2 and participated in target gene, SNM2, alternative splicing involved in AGO2 by the indirect interaction with AGO2, which produced different transcripts of SMN2 in discrepant expression level. This study laid important experiment foundation for the further analysis of the nuclear functions of gene silencing components.

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RNA duplexes in transcriptional regulation

BioMolecular Concepts ◽

10.1515/bmc.2010.021 ◽

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.

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small RNA can move long distances through plant vasculature to influence gene expression in shoot apical meristems

10.1101/2021.09.20.460861 ◽

2021 ◽

Author(s):

Mark A. A. Minow ◽

Viktoriya Coneva ◽

Victoria Lesy ◽

Max Misyura ◽

Joseph Colasanti

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Gene Silencing ◽

Small Rna ◽

Separate Experiment ◽

Transcriptional Gene Silencing ◽

Long Distance ◽

Regulate Gene Expression ◽

Post Transcriptional Gene Silencing ◽

Influence Gene Expression

AbstractIn plants, small RNA (sRNA) can regulate gene expression via post transcriptional gene silencing (PTGS) or through RNA-directed DNA methylation (RdDM) leading to transcriptional gene silencing (TGS). sRNA is mobile throughout the plant, with movement occurring short distances from cell-to-cell as well as long distances through the vasculature via phloem trafficking. The range of long-distance sRNA mediated signaling from the vasculature to the shoot apical meristem (SAM) is not clear. To investigate this, two independent transgenic approaches were used to examine trafficking of phloem-expressed sRNA to the SAM in Arabidopsis thaliana. First, the phloem companion-cell specific promoter SUC2 was used to drive expression of an inverted repeat complementary to FLOWERING LOCUS D (FD), a flowering time regulator expressed exclusively in the SAM. In a separate experiment, the SUC2 promoter was used to express an artificial microRNA (aMiR) designed to target a synthetic CLAVATA3 (CLV3) target in the SAM stem cells. Both systems provide evidence of a phloem-to-SAM sRNA communication axis connecting distal regions of the plant to the stem cells of the SAM, which ultimately gives rise to all shoot tissues, including gametes. Thus, phloem-to-SAM sRNA movement defines an important link between sRNA expressed in distal regions of the plant and the growing shoot. Importantly, phloem-to-SAM sRNA trafficking may allow somatic sRNA to direct SAM RdDM, fixing transient sRNA expression events into stable epigenetic changes.

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Dimethylated H3K27 Is a Repressive Epigenetic Histone Mark in the Protist Entamoeba histolytica and Is Significantly Enriched in Genes Silenced via the RNAi Pathway

Journal of Biological Chemistry ◽

10.1074/jbc.m115.647263 ◽

2015 ◽

Vol 290 (34) ◽

pp. 21114-21130 ◽

Cited By ~ 22

Author(s):

Bardees M. Foda ◽

Upinder Singh

Keyword(s):

Gene Silencing ◽

Histone Modification ◽

Entamoeba Histolytica ◽

Transcriptional Repression ◽

Small Rnas ◽

Regulation Of Gene Expression ◽

Histone Mark ◽

Rnai Pathway ◽

Transcriptional Gene Silencing ◽

Chromosomal Loci

RNA interference (RNAi) is a fundamental biological process that plays a crucial role in regulation of gene expression in many organisms. Transcriptional gene silencing (TGS) is one of the important nuclear roles of RNAi. Our previous data show that Entamoeba histolytica has a robust RNAi pathway that links to TGS via Argonaute 2-2 (Ago2-2) associated 27-nucleotide small RNAs with 5′-polyphosphate termini. Here, we report the first repressive histone mark to be identified in E. histolytica, dimethylation of H3K27 (H3K27Me2), and demonstrate that it is enriched at genes that are silenced by RNAi-mediated TGS. An RNAi-silencing trigger can induce H3K27Me2 deposits at both episomal and chromosomal loci, mediating gene silencing. Our data support two phases of RNAi-mediated TGS: an active silencing phase where the RNAi trigger is present and both H3K27Me2 and Ago2-2 concurrently enrich at chromosomal loci; and an established silencing phase in which the RNAi trigger is removed, but gene silencing with H3K27Me2 enrichment persist independently of Ago2-2 deposition. Importantly, some genes display resistance to chromosomal silencing despite induction of functional small RNAs. In those situations, the RNAi-triggering plasmid that is maintained episomally gets partially silenced and has H3K27Me2 enrichment, but the chromosomal copy displays no repressive histone enrichment. Our data are consistent with a model in which H3K27Me2 is a repressive histone modification, which is strongly associated with transcriptional repression. This is the first example of an epigenetic histone modification that functions to mediate RNAi-mediated TGS in the deep-branching eukaryote E. histolytica.

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