Non-Coding RNAs: A Dynamic and Complex Network of Gene Regulation

Munshi, Anjana; Mohan, .; Yr, Ahuja

doi:10.4172/2153-0645.1000156

J Pharmacogenomics Pharmacoproteomics

2016

DOI: 10.4172/2153-0645.1000156

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Non-Coding RNAs: A Dynamic and Complex Network of Gene Regulation

Anjana Munshi¹,

. Mohan²,

Ahuja Yr³

Abstract: It has been estimated that less than two percent of the mammalian genome encodes proteins, rest of the genome which was earlier considered as junk DNA is the treasure trove of non-coding RNAs (ncRNAs). Many ncRNAs have now been characterized. They constitute one of the largest families of gene regulators that are found in plants and animals. They form a complex network and have key roles in diverse regulatory pathways involved in human health and disease. In this review, different types of ncRNAs, their biogen… Show more

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Cited by 3 publications

References 158 publications

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Extracellular RNA in viral–host interactions: Thinking outside the cell

et al. 2019

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Small RNAs and their associated RNA interference (RNAi) pathways underpin diverse mechanisms of gene regulation and genome defense across all three kingdoms of life and are integral to virus–host interactions. In plants, fungi and many animals, an ancestral RNAi pathway exists as a host defense mechanism whereby viral double‐stranded RNA is processed to small RNAs that enable recognition and degradation of the virus. While this antiviral RNAi pathway is not generally thought to be present in mammals, other RNAi mechanisms can influence infection through both viral‐ and host‐derived small RNAs. Furthermore, a burgeoning body of data suggests that small RNAs in mammals can function in a non‐cell autonomous manner to play various roles in cell‐to‐cell communication and disease through their transport in extracellular vesicles. While vesicular small RNAs have not been proposed as an antiviral defense pathway per se, there is increasing evidence that the export of host‐ or viral‐derived RNAs from infected cells can influence various aspects of the infection process. This review discusses the current knowledge of extracellular RNA functions in viral infection and the technical challenges surrounding this field of research. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA in Disease and Development > RNA in Disease Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action

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Extracellular RNA in viral–host interactions: Thinking outside the cell

et al. 2019

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InDePTH: detection of hub genes for developing gene expression networks under anticancer drug treatment

et al. 2018

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It has been difficult to elucidate the structure of gene regulatory networks under anticancer drug treatment. Here, we developed an algorithm to highlight the hub genes that play a major role in creating the upstream and downstream relationships within a given set of differentially expressed genes. The directionality of the relationships between genes was defined using information from comprehensive collections of transcriptome profiles after gene knockdown and overexpression. As expected, among the drug-perturbed genes, our algorithm tended to derive plausible hub genes, such as transcription factors. Our validation experiments successfully showed the anticipated activity of certain hub gene in establishing the gene regulatory network that was associated with cell growth inhibition. Notably, giving such top priority to the hub gene was not achieved by ranking fold change in expression and by the conventional gene set enrichment analysis of drug-induced transcriptome data. Thus, our data-driven approach can facilitate to understand drug-induced gene regulatory networks for finding potential functional genes.

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Trends of non-coding RNAs research in acute rejection after kidney transplantation

Ghods¹

2019

Non-coding RNA Investig

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Non-Coding RNAs: A Dynamic and Complex Network of Gene Regulation

Cited by 3 publications

References 158 publications

Extracellular RNA in viral–host interactions: Thinking outside the cell

Extracellular RNA in viral–host interactions: Thinking outside the cell

InDePTH: detection of hub genes for developing gene expression networks under anticancer drug treatment

Trends of non-coding RNAs research in acute rejection after kidney transplantation

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