Special Issue "Non-coding RNA"

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A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: closed (31 December 2012)

Special Issue Editors

Guest Editor
Prof. Dr. Ling-Ling Chen (Website)

Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-yang Road, Shanghai 200031, China
Fax: +86 21 5492 1011
Interests: noncoding RNAs; RNA editing; gene expression regulation; stem cell biology
Guest Editor
Dr. Yuntao (Steve) Mao

Department of Chemistry and Chemical Biology, Harvard University 12 Oxford St, Cambridge, MA 02138, USA
Interests: noncoding RNAs; mammalian nuclear organization; single-cell sequencing; cancer biology

Special Issue Information

Dear Colleagues,

RNA has long been known to connect genes and proteins through gene transcription and protein translation. Recently, small noncoding RNAs, such as siRNAs, microRNAs, and piRNAs, have been demonstrated to play important roles in many aspects of gene regulation. New classes of noncoding RNAs, long noncoding RNAs in particular, have lately been identified and functionally characterized. The centrality of RNA in fundamental cellular processes is now highly appreciated. This issue intends to glance the recent history of noncoding RNAs and to showcase their regulatory roles in gene expression at multiple levels. Therefore, we invite submission of high quality review manuscripts that cover any aspect of the biochemistry, biophysics, cell biology, genetics, physiology, disease, and evolution of both small and long noncoding RNAs, viral and bacterial RNAs, and other regulatory RNAs.
We look forward to your contributions.

Prof. Dr. Ling-Ling Chen
Dr. Yuntao (Steve) Mao
Guest Editors

Keywords

  • noncoding RNAs
  • chromosome
  • epigenetics
  • gene expression regulation

Published Papers (4 papers)

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Review

Open AccessReview Single Nucleotide Polymorphisms Associated with MicroRNA Regulation
Biomolecules 2013, 3(2), 287-302; doi:10.3390/biom3020287
Received: 2 March 2013 / Revised: 22 March 2013 / Accepted: 27 March 2013 / Published: 9 April 2013
Cited by 11 | PDF Full-text (235 KB) | HTML Full-text | XML Full-text
Abstract
Since the discovery of microRNA (miRNA), the polymorphisms that affect miRNA regulation had been extensively investigated by many independent studies. Recently, researchers utilized bioinformatics and statistical approaches for genome-wide analysis on the human polymorphisms that reside in the miRNA genes, targets, and/or [...] Read more.
Since the discovery of microRNA (miRNA), the polymorphisms that affect miRNA regulation had been extensively investigated by many independent studies. Recently, researchers utilized bioinformatics and statistical approaches for genome-wide analysis on the human polymorphisms that reside in the miRNA genes, targets, and/or genes involved in miRNA processing. In this review, we will give an overview about the important findings of these studies from three perspectives: architecture of the polymorphisms within miRNAs or their targets, potential functional consequences of the polymorphisms on miRNA processing or targeting, and the associations of the polymorphisms with miRNA or target gene expression. The results of the previous studies demonstrated the signatures of natural selections on the miRNA genes and their targets, and proposed a collection of potentially functional, expression-associated, and/or positively selected polymorphisms that are promising for further investigations. In the meantime, a few useful resources about the polymorphic miRNA regulation have been developed and the different features of these databases were discussed in this review. Though recent research had benefited from these comprehensive studies and resources, there were still gaps in our knowledge about the polymorphisms involved in miRNA regulation, and future investigations were expected to address these questions. Full article
(This article belongs to the Special Issue Non-coding RNA)
Open AccessReview Panning for Long Noncoding RNAs
Biomolecules 2013, 3(1), 226-241; doi:10.3390/biom3010226
Received: 18 December 2012 / Revised: 21 February 2013 / Accepted: 21 February 2013 / Published: 28 February 2013
Cited by 4 | PDF Full-text (365 KB) | HTML Full-text | XML Full-text
Abstract
The recent advent of high-throughput approaches has revealed widespread transcription of the human genome, leading to a new appreciation of transcription regulation, especially from noncoding regions. Distinct from most coding and small noncoding RNAs, long noncoding RNAs (lncRNAs) are generally expressed at [...] Read more.
The recent advent of high-throughput approaches has revealed widespread transcription of the human genome, leading to a new appreciation of transcription regulation, especially from noncoding regions. Distinct from most coding and small noncoding RNAs, long noncoding RNAs (lncRNAs) are generally expressed at low levels, are less conserved and lack protein-coding capacity. These intrinsic features of lncRNAs have not only hampered their full annotation in the past several years, but have also generated controversy concerning whether many or most of these lncRNAs are simply the result of transcriptional noise. Here, we assess these intrinsic features that have challenged lncRNA discovery and further summarize recent progress in lncRNA discovery with integrated methodologies, from which new lessons and insights can be derived to achieve better characterization of lncRNA expression regulation. Full annotation of lncRNA repertoires and the implications of such annotation will provide a fundamental basis for comprehensive understanding of pervasive functions of lncRNAs in biological regulation. Full article
(This article belongs to the Special Issue Non-coding RNA)
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Open AccessReview MicroRNA Expression in Cystic Fibrosis Airway Epithelium
Biomolecules 2013, 3(1), 157-167; doi:10.3390/biom3010157
Received: 14 January 2013 / Revised: 1 February 2013 / Accepted: 3 February 2013 / Published: 11 February 2013
PDF Full-text (152 KB) | HTML Full-text | XML Full-text
Abstract
MicroRNAs (miRs) have emerged as major regulators of the protein content of a cell. In the most part, miRs negatively regulate target mRNA expression, with sets of miRs predicted to regulate certain signaling pathways. The miR expression profile of endobronchial brushings is [...] Read more.
MicroRNAs (miRs) have emerged as major regulators of the protein content of a cell. In the most part, miRs negatively regulate target mRNA expression, with sets of miRs predicted to regulate certain signaling pathways. The miR expression profile of endobronchial brushings is altered in people with cystic fibrosis (CF) compared to those without CF. How this impacts on CF has important implications for our growing understanding of the pathophysiology of CF lung disease and the development of new therapeutics to treat its pulmonary manifestations. Herein we discuss the potential consequences of altered miR expression in CF airway epithelium particularly with respect to cystic fibrosis transmembrane conductance regulator (CFTR) expression, innate immunity and toll-like receptor signalling and explore how best to exploit these changes for therapeutic benefit. Full article
(This article belongs to the Special Issue Non-coding RNA)
Open AccessReview Emerging Roles for Non-Coding RNAs in Male Reproductive Development in Flowering Plants
Biomolecules 2012, 2(4), 608-621; doi:10.3390/biom2040608
Received: 26 October 2012 / Revised: 19 November 2012 / Accepted: 23 November 2012 / Published: 4 December 2012
Cited by 2 | PDF Full-text (577 KB) | HTML Full-text | XML Full-text
Abstract
Knowledge of sexual reproduction systems in flowering plants is essential to humankind, with crop fertility vitally important for food security. Here, we review rapidly emerging new evidence for the key importance of non-coding RNAs in male reproductive development in flowering plants. From [...] Read more.
Knowledge of sexual reproduction systems in flowering plants is essential to humankind, with crop fertility vitally important for food security. Here, we review rapidly emerging new evidence for the key importance of non-coding RNAs in male reproductive development in flowering plants. From the commitment of somatic cells to initiating reproductive development through to meiosis and the development of pollen—containing the male gametes (sperm cells)—in the anther, there is now overwhelming data for a diversity of non-coding RNAs and emerging evidence for crucial roles for them in regulating cellular events at these developmental stages. A particularly exciting development has been the association of one example of cytoplasmic male sterility, which has become an unparalleled breeding tool for producing new crop hybrids, with a non-coding RNA locus. Full article
(This article belongs to the Special Issue Non-coding RNA)
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