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Phenotypic noise: effects of post‐transcriptional regulatory processes affecting mRNA

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The inherently stochastic nature of biomolecular processes is one of the main sources giving rise to cell‐to‐cell variations in protein and mRNA abundance, termed noise. Noise in isogenic populations can enhance survival under adverse conditions and stress, and has therefore played a fundamental role in evolution. On the other hand, noise may have detrimental effects and therefore cells must also display robustness to fluctuations and possess mechanisms of control in order to function properly. Noise can be introduced at every step in the cascade of intermediate events resulting in the production of functional proteins. While initial studies of noise focused on stochasticity introduced at the transcriptional level, recent years have witnessed a gradual shift of emphasis into the effects that post‐transcriptional processes have on phenotypic noise. Here, we survey the insights that have been gained on the effects of processes that modify RNA transcript populations on phenotypic noise, including regulation by noncoding RNAs in prokaryotes and eukaryotes, alternative splicing and transcriptional interference. WIREs RNA 2014, 5:197–207. doi: 10.1002/wrna.1209 This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes RNA Processing > RNA Editing and Modification Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA in Disease and Development > RNA in Development

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Downregulation of gene expression by noncoding small‐interfering RNAs (siRNAs) and microRNAs (miRNAs). (a) An Argonaute protein binds a ∼22‐nucleotide‐long RNA sequence known as the guide, forming the RNA‐induced silencing complex (RISC), which exhibits sequence specificity. The RISC binds target messenger RNAs (mRNAs) by the formation of Watson–Crick pairs between the seed sequence in the guide and the target with full or partial complementarity in the siRNAs and miRNAs cases, respectively, and downregulates gene expression by either cutting the target or by blocking translation. (b) Ubiquitous coherent and incoherent feed‐forward loop (FFL) motifs in which miRNAs are found within genetic networks. There are overall four possible types of coherent and incoherent FFLs each.
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Regulation of gene expression by small RNAs (sRNAs). (a) Common mechanisms of sRNA function, including discoordinate regulation in which portion of a transcript is degraded, while the rest is protected by a secondary structure and translated. Orange wedged circles represent the RNase E degradosome pathway and magenta rectangles represent the ribosome‐binding sites (RBS). (b) The embedding of sRNAs within genetic networks in which extrinsic sources are dominant can be viewed as formation of an incoherent feed‐forward loop (FFL) motif in which transcriptional extrinsic sources act directly on the expression of target genes and indirectly via an sRNA. A typical example is furnished by the sRNA RyhB. Other sRNAs (e.g., RybB) form mixed incoherent FFLs along with transcription factors (TFs).
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Mechanisms of transcriptional interference for convergent promoters. Most typically, RNA polymerases (RNAPs) transcribe from a pair of strong (aggressive) and weak (sensitive) promoters (pA and pS, respectively). All mechanisms apply for tandem promoters as well (when both promoters direct transcription in the same direction), except for collisions.
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Different modalities of alternative splicing. (a) Shown are exon skipping, alternative acceptor‐site selection, alternative donor‐site selection, and intron retention. Constitutive exons (blue); alternatively spliced regions (orange); and introns and splicing options are represented by solid lines and by dashed lines, respectively. (b) Alternative splicing of the MKNK2 gene into isoforms Mnk2a and Mnk2b, illustrating the alternative 3′ splice‐site mechanism and the variation of isoforms in individual cells. (The scheme is adapted from Ref. )
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RNA in Disease and Development > RNA in Development
Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
RNA Processing > RNA Editing and Modification
RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes

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