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Genes 2018, 9(3), 141; https://doi.org/10.3390/genes9030141

The Non-Coding Regulatory RNA Revolution in Archaea

Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
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Received: 24 January 2018 / Revised: 20 February 2018 / Accepted: 22 February 2018 / Published: 5 March 2018
(This article belongs to the Special Issue Genetics and Genomics of Extremophiles)
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Abstract

Small non-coding RNAs (sRNAs) are ubiquitously found in the three domains of life playing large-scale roles in gene regulation, transposable element silencing and defense against foreign elements. While a substantial body of experimental work has been done to uncover function of sRNAs in Bacteria and Eukarya, the functional roles of sRNAs in Archaea are still poorly understood. Recently, high throughput studies using RNA-sequencing revealed that sRNAs are broadly expressed in the Archaea, comprising thousands of transcripts within the transcriptome during non-challenged and stressed conditions. Antisense sRNAs, which overlap a portion of a gene on the opposite strand (cis-acting), are the most abundantly expressed non-coding RNAs and they can be classified based on their binding patterns to mRNAs (3′ untranslated region (UTR), 5′ UTR, CDS-binding). These antisense sRNAs target many genes and pathways, suggesting extensive roles in gene regulation. Intergenic sRNAs are less abundantly expressed and their targets are difficult to find because of a lack of complete overlap between sRNAs and target mRNAs (trans-acting). While many sRNAs have been validated experimentally, a regulatory role has only been reported for very few of them. Further work is needed to elucidate sRNA-RNA binding mechanisms, the molecular determinants of sRNA-mediated regulation, whether protein components are involved and how sRNAs integrate with complex regulatory networks. View Full-Text
Keywords: small RNAs; sRNAs; non-coding RNAs; ncRNAs; archaea; stress response; gene regulation; RNA-seq small RNAs; sRNAs; non-coding RNAs; ncRNAs; archaea; stress response; gene regulation; RNA-seq
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).
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Gelsinger, D.R.; DiRuggiero, J. The Non-Coding Regulatory RNA Revolution in Archaea. Genes 2018, 9, 141.

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