期刊
GENES
卷 9, 期 6, 页码 -出版社
MDPI
DOI: 10.3390/genes9060302
关键词
long-range; RNA structure; folding; RNA-RNA interaction; mutually exclusive splicing; RNA processing; polyadenylation; Dscam; Nmnat; DST
资金
- Skolkovo Institute of Science and Technology [RF-0000000653]
The ability to form an intramolecular structure plays a fundamental role in eukaryotic RNA biogenesis. Proximate regions in the primary transcripts fold into a local secondary structure, which is then hierarchically assembled into a tertiary structure that is stabilized by RNA-binding proteins and long-range intramolecular base pairings. While the local RNA structure can be predicted reasonably well for short sequences, long-range structure at the scale of eukaryotic genes remains problematic from the computational standpoint. The aim of this review is to list functional examples of long-range RNA structures, to summarize current comparative methods of structure prediction, and to highlight their advances and limitations in the context of long-range RNA structures. Most comparative methods implement the first-align-then-fold principle, i.e., they operate on multiple sequence alignments, while functional RNA structures often reside in non-conserved parts of the primary transcripts. The opposite first-fold-then-align approach is currently explored to a much lesser extent. Developing novel methods in both directions will improve the performance of comparative RNA structure analysis and help discover novel long-range structures, their higher-order organization, and RNA-RNA interactions across the transcriptome.
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