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Tackling Structures of Long Noncoding RNAs
Los Alamos National Laboratory, Los Alamos, NM 87545, USA
* Author to whom correspondence should be addressed.
Received: 16 October 2013; in revised form: 15 November 2013 / Accepted: 25 November 2013 / Published: 4 December 2013
Abstract: RNAs are important catalytic machines and regulators at every level of gene expression. A new class of RNAs has emerged called long non-coding RNAs, providing new insights into evolution, development and disease. Long non-coding RNAs (lncRNAs) predominantly found in higher eukaryotes, have been implicated in the regulation of transcription factors, chromatin-remodeling, hormone receptors and many other processes. The structural versatility of RNA allows it to perform various functions, ranging from precise protein recognition to catalysis and metabolite sensing. While major housekeeping RNA molecules have long been the focus of structural studies, lncRNAs remain the least characterized class, both structurally and functionally. Here, we review common methodologies used to tackle RNA structure, emphasizing their potential application to lncRNAs. When considering the complexity of lncRNAs and lack of knowledge of their structure, chemical probing appears to be an indispensable tool, with few restrictions in terms of size, quantity and heterogeneity of the RNA molecule. Probing is not constrained to in vitro analysis and can be adapted to high-throughput sequencing platforms. Significant efforts have been applied to develop new in vivo chemical probing reagents, new library construction protocols for sequencing platforms and improved RNA prediction software based on the experimental evidence.
Keywords: long noncoding RNAs; lncRNAs; secondary structure; chemical probing; SHAPE; epigenetics
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MDPI and ACS Style
Novikova, I.V.; Hennelly, S.P.; Sanbonmatsu, K.Y. Tackling Structures of Long Noncoding RNAs. Int. J. Mol. Sci. 2013, 14, 23672-23684.
Novikova IV, Hennelly SP, Sanbonmatsu KY. Tackling Structures of Long Noncoding RNAs. International Journal of Molecular Sciences. 2013; 14(12):23672-23684.
Novikova, Irina V.; Hennelly, Scott P.; Sanbonmatsu, Karissa Y. 2013. "Tackling Structures of Long Noncoding RNAs." Int. J. Mol. Sci. 14, no. 12: 23672-23684.