Gene regulation by non-coding RNAs

Patil, Veena S.; Zhou, Rui; Rana, Tariq M.

doi:10.3109/10409238.2013.844092

Cited by 156 publications

(115 citation statements)

References 231 publications

(299 reference statements)

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“…If siRNAs and mRNAs possess completely complementary sequences, then sequence-specific cleavage takes place by RISC negotiation. However, limit complementarity to the cognate gene sequence results in RNA degradation through miRNA activity 18 . Consequently, prior to administration, large-scale siRNA screening is usually performed to characterize both potential targets and the most effective siRNA sequence.…”

Section: Main Textmentioning

confidence: 99%

Stimuli-Responsive Mesoporous Silica NPs as Non-viral Dual siRNA/Chemotherapy Carriers for Triple Negative Breast Cancer

Darvishi

Farahmand

Majidzadeh‐A

2017

Molecular Therapy - Nucleic Acids

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Triple negative breast cancer (TNBC) is the most aggressive and lethal subtype of breast cancer. It is associated with a very poor prognosis and intrinsically resistant to several conventional and targeted chemotherapy agents and has a 5-year survival rate of less than 25%. Because the treatment options for TNBC are very limited and not efficient enough for achieving minimum desired goals, shifting toward a new generation of anti-cancer agents appears to be very critical. Among recent alternative approaches being proposed, small interfering RNA (siRNA) gene therapy can potently suppress Bcl-2 proto-oncogene and p-glycoprotein gene expression, the most important chemotherapy resistance inducers in TNBC. When resensitized, primarily ineffective chemotherapy drugs turn back into valuable sources for further intensive chemotherapy. Regrettably, siRNA’s poor stability, rapid clearance in the circulatory system, and poor cellular uptake mostly hampers the beneficial outcomes of siRNA therapy. Considering these drawbacks, dual siRNA/chemotherapy drug encapsulation in targeted delivery vehicles, especially mesoporous silica nanoparticles (MSNs) appears to be the most reasonable solution. The literature is full of reports of successful treatments of multi-drug-resistant cancer cells by administration of dual drug/siRNA-loaded MSNs. Here we tried to answer the question of whether application of a similar approach with identical delivery devices in TNBC is rational.

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Section: Main Textmentioning

confidence: 99%

Stimuli-Responsive Mesoporous Silica NPs as Non-viral Dual siRNA/Chemotherapy Carriers for Triple Negative Breast Cancer

Darvishi

Farahmand

Majidzadeh‐A

2017

Molecular Therapy - Nucleic Acids

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“…The role of exRNAs in such processes is suggested by the relatively high content of regulatory RNAs in EVs. Deep sequencing of RNA from EVs derived from different cell types reveals substantial levels of many small ncRNAs, as well as lncRNAs, both of which are implicated in gene regulation [for review see 79]. These include miRNAs, as well as signal recognition particle (SRP)-RNA, vault RNA, Y-RNA and transfer RNA (tRNA) fragments in EVs from dendritic cells [59]; 7SL, Y-RNA and piRNA in EVs from a neural cell line [47]; and lncRNA, piRNA, tRNA fragments and snoRNA in EVs from plasma of glioma patients [49].…”

Section: Diversity Of Rna Molecules In Evsmentioning

confidence: 99%

Extracellular RNA mediates and marks cancer progression

Redzic

Balaj

Vos

et al. 2014

Seminars in Cancer Biology

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Different types of RNAs identified thus far represent a diverse group of macromolecules that are involved in the regulation of different biological processes. RNA is generally thought to be localized primarily in the nucleus and cytoplasm, however, some types of RNA have been detected in the extracellular milieu. These extracellular RNA (exRNA) molecules are protected from degradation and it is now widely accepted that extracellular vesicles and ribonucleoprotein particles serve as transport vehicles for exRNA among cells. The functional consequence of this transfer of genetic information probably encompasses a broad range of normal developmental and physiologic processes in many organisms. This review will focus on the role of exRNA communication in cancer. We will focus on different types of RNA species identified and characterized within tumor-derived extracellular vesicles. Further, we will describe the role of exRNAs in cancer progression, as well as their potential for use as diagnostic biomarkers and therapeutic tools for monitoring and treating cancer, respectively.

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“…This collective term encompasses different types of transcripts such as ribosomal, transfer, and other housekeeping RNAs [e.g., signal recognition particle (SRP) and RNase P RNA components, tmRNA, or CRISPR RNAs], and also many regulatory RNA species. The latter group is particularly vast and heterogeneous, and several new classes, such as siRNAs, micro RNAs (miRNAs), PIWI-interacting RNAs (piRNAs), long noncoding RNAs, and various bacterial regulatory small RNAs (sRNAs), have emerged as important modulators of gene expression (3,4).…”

mentioning

confidence: 99%

Grad-seq guides the discovery of ProQ as a major small RNA-binding protein

Smirnov

Förstner

Holmqvist

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

273

465

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The functional annotation of transcriptomes and identification of noncoding RNA (ncRNA) classes has been greatly facilitated by the advent of next-generation RNA sequencing which, by reading the nucleotide order of transcripts, theoretically allows the rapid profiling of all transcripts in a cell. However, primary sequence per se is a poor predictor of function, as ncRNAs dramatically vary in length and structure and often lack identifiable motifs. Therefore, to visualize an informative RNA landscape of organisms with potentially new RNA biology that are emerging from microbiome and environmental studies requires the use of more functionally relevant criteria. One such criterion is the association of RNAs with functionally important cognate RNA-binding proteins. Here we analyze the full ensemble of cellular RNAs using gradient profiling by sequencing (Grad-seq) in the bacterial pathogen Salmonella enterica, partitioning its coding and noncoding transcripts based on their network of RNA-protein interactions. In addition to capturing established RNA classes based on their biochemical profiles, the Grad-seq approach enabled the discovery of an overlooked large collective of structured small RNAs that form stable complexes with the conserved protein ProQ. We show that ProQ is an abundant RNA-binding protein with a wide range of ligands and a global influence on Salmonella gene expression. Given its generic ability to chart a functional RNA landscape irrespective of transcript length and sequence diversity, Grad-seq promises to define functional RNA classes and major RNA-binding proteins in both model species and genetically intractable organisms.small RNA | noncoding RNA | RNA-protein interaction | ProQ | Hfq

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Gene regulation by non-coding RNAs

Cited by 156 publications

References 231 publications

Stimuli-Responsive Mesoporous Silica NPs as Non-viral Dual siRNA/Chemotherapy Carriers for Triple Negative Breast Cancer

Stimuli-Responsive Mesoporous Silica NPs as Non-viral Dual siRNA/Chemotherapy Carriers for Triple Negative Breast Cancer

Extracellular RNA mediates and marks cancer progression

Grad-seq guides the discovery of ProQ as a major small RNA-binding protein

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