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      RNA Regulatory Networks as a Control of Stochasticity in Biological Systems

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          Abstract

          The discovery that the non-protein coding part of human genome, dismissed as “junk DNA,” is actively transcripted and carries out crucial functions is probably one of the most important discoveries of the past decades. These transcripts are becoming the rising stars of modern biology. In this review, we have casted a new light on RNAs. We have placed these molecules in the context of life origins, evolution with a big emphasize on the “RNA networks” concept. We discuss how this view can help us to understand the global role of RNA networks in modern cells, and can change our perception of the cell biology and therapy. Finally, although high-throughput methods as well as traditional case-to-case studies have laid the groundwork for our current knowledge of transcriptomes, we would like to discuss new strategies that are better suited to uncover and tackle these integrated and complex RNA networks.

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          Most cited references61

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          Nature, nurture, or chance: stochastic gene expression and its consequences.

          Gene expression is a fundamentally stochastic process, with randomness in transcription and translation leading to cell-to-cell variations in mRNA and protein levels. This variation appears in organisms ranging from microbes to metazoans, and its characteristics depend both on the biophysical parameters governing gene expression and on gene network structure. Stochastic gene expression has important consequences for cellular function, being beneficial in some contexts and harmful in others. These situations include the stress response, metabolism, development, the cell cycle, circadian rhythms, and aging.
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            Stochasticity in gene expression: from theories to phenotypes.

            Genetically identical cells exposed to the same environmental conditions can show significant variation in molecular content and marked differences in phenotypic characteristics. This variability is linked to stochasticity in gene expression, which is generally viewed as having detrimental effects on cellular function with potential implications for disease. However, stochasticity in gene expression can also be advantageous. It can provide the flexibility needed by cells to adapt to fluctuating environments or respond to sudden stresses, and a mechanism by which population heterogeneity can be established during cellular differentiation and development.
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              Regulatory RNAs in bacteria.

              Bacteria possess numerous and diverse means of gene regulation using RNA molecules, including mRNA leaders that affect expression in cis, small RNAs that bind to proteins or base pair with target RNAs, and CRISPR RNAs that inhibit the uptake of foreign DNA. Although examples of RNA regulators have been known for decades in bacteria, we are only now coming to a full appreciation of their importance and prevalence. Here, we review the known mechanisms and roles of regulatory RNAs, highlight emerging themes, and discuss remaining questions.
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                Author and article information

                Contributors
                Journal
                Front Genet
                Front Genet
                Front. Genet.
                Frontiers in Genetics
                Frontiers Media S.A.
                1664-8021
                07 May 2019
                2019
                : 10
                : 403
                Affiliations
                InBioS – Center for Protein Engineering, University of Liège , Liège, Belgium
                Author notes

                Edited by: Graziano Pesole, University of Bari Aldo Moro, Italy

                Reviewed by: Ernesto Picardi, University of Bari Aldo Moro, Italy; Scott A. Tenenbaum, University at Albany, United States

                *Correspondence: Marylène Vandevenne, mvandevenne@ 123456uliege.be

                This article was submitted to RNA, a section of the journal Frontiers in Genetics

                Article
                10.3389/fgene.2019.00403
                6514243
                31134128
                ad51ad5f-2b8d-4cf2-b971-524fc1fff48e
                Copyright © 2019 Vandevenne, Delmarcelle and Galleni.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 08 February 2019
                : 12 April 2019
                Page count
                Figures: 2, Tables: 0, Equations: 0, References: 83, Pages: 8, Words: 0
                Categories
                Genetics
                Review

                Genetics
                regulatory rna networks,non-coding rnas,cell stochasticity/determinism,rna world theories,origins of life

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