Next Article in Journal
Integrative Analysis of Dysregulated lncRNA-Associated ceRNA Network Reveals Functional lncRNAs in Gastric Cancer
Next Article in Special Issue
An Evolutionary Mechanism for the Generation of Competing RNA Structures Associated with Mutually Exclusive Exons
Previous Article in Journal
Decision Variants for the Automatic Determination of Optimal Feature Subset in RF-RFE
Previous Article in Special Issue
Automated Recognition of RNA Structure Motifs by Their SHAPE Data Signatures
Open AccessReview

Towards Long-Range RNA Structure Prediction in Eukaryotic Genes

1
Skolkovo Institute for Science and Technology, Ulitsa Nobelya 3, Moscow 121205, Russia
2
The Faculty of Bioengineering and Bioinformatics, Moscow State University 1-73, Moscow 119899, Russia
3
Faculty of Computer Science, Higher School of Economics, Kochnovskiy Proyezd 3, Moscow 125319, Russia
Genes 2018, 9(6), 302; https://doi.org/10.3390/genes9060302
Received: 27 April 2018 / Revised: 13 June 2018 / Accepted: 13 June 2018 / Published: 15 June 2018
(This article belongs to the Special Issue Computational Analysis of RNA Structure and Function)
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. View Full-Text
Keywords: long-range; RNA structure; folding; RNA–RNA interaction; mutually exclusive splicing; RNA processing; polyadenylation; Dscam; Nmnat; DST long-range; RNA structure; folding; RNA–RNA interaction; mutually exclusive splicing; RNA processing; polyadenylation; Dscam; Nmnat; DST
Show Figures

Figure 1

MDPI and ACS Style

Pervouchine, D.D. Towards Long-Range RNA Structure Prediction in Eukaryotic Genes. Genes 2018, 9, 302.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop