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Methods. 2017 May 1;120:3-16. doi: 10.1016/j.ymeth.2017.04.009. Epub 2017 Apr 20.

In silico methods for co-transcriptional RNA secondary structure prediction and for investigating alternative RNA structure expression.

Author information

1
Laboratory of Bioinformatics of RNA Structure and Transcriptome Regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin-Buch, Germany; Institute of Chemistry and Biochemistry, Free University, Thielallee 63, 14195 Berlin, Germany. Electronic address: irmtraud.meyer@cantab.net.

Abstract

RNA transcripts are the primary products of active genes in any living organism, including many viruses. Their cellular destiny not only depends on primary sequence signals, but can also be determined by RNA structure. Recent experimental evidence shows that many transcripts can be assigned more than a single functional RNA structure throughout their cellular life and that structure formation happens co-transcriptionally, i.e. as the transcript is synthesised in the cell. Moreover, functional RNA structures are not limited to non-coding transcripts, but can also feature in coding transcripts. The picture that now emerges is that RNA structures constitute an additional layer of information that can be encoded in any RNA transcript (and on top of other layers of information such as protein-context) in order to exert a wide range of functional roles. Moreover, different encoded RNA structures can be expressed at different stages of a transcript's life in order to alter the transcript's behaviour depending on its actual cellular context. Similar to the concept of alternative splicing for protein-coding genes, where a single transcript can yield different proteins depending on cellular context, it is thus appropriate to propose the notion of alternative RNA structure expression for any given transcript. This review introduces several computational strategies that my group developed to detect different aspects of RNA structure expression in vivo. Two aspects are of particular interest to us: (1) RNA secondary structure features that emerge during co-transcriptional folding and (2) functional RNA structure features that are expressed at different times of a transcript's life and potentially mutually exclusive.

KEYWORDS:

Co-transcriptional folding; Prediction algorithms; RNA folding pathways; RNA secondary structures; RNA structure prediction

PMID:
28433606
DOI:
10.1016/j.ymeth.2017.04.009
[Indexed for MEDLINE]

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