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RNA Secondary Structure Prediction Using High-throughput SHAPE

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Towards Long-Range RNA Structure Prediction in Eukaryotic Genes.

Dmitri D Pervouchine^1,2,3

¹Skolkovo Institute for Science and Technology, Ulitsa Nobelya 3, Moscow 121205, Russia. d.pervouchine@skoltech.ru.

|June 20, 2018

Summary

Predicting long-range RNA structures in eukaryotes is challenging. This review explores functional examples and computational methods, highlighting limitations and future directions for RNA structure analysis.

Keywords:

DST Dscam Nmnat RNA processing RNA structure RNA–RNA interaction folding long-range mutually exclusive splicing polyadenylation

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Area of Science:

Molecular Biology
Computational Biology
Genomics

Background:

Intramolecular RNA structures are crucial for eukaryotic RNA biogenesis, involving local secondary and tertiary folding.
Predicting local RNA structures is feasible for short sequences, but long-range structures in eukaryotic genes pose significant computational challenges.

Purpose of the Study:

To review functional examples of long-range RNA structures in eukaryotes.
To summarize and critically evaluate current comparative methods for RNA structure prediction.
To identify advances and limitations in predicting long-range RNA structures.

Main Methods:

Review of existing literature on functional long-range RNA structures.
Analysis of comparative RNA structure prediction methods, focusing on the 'first-align-then-fold' approach.
Exploration of the less-explored 'first-fold-then-align' strategy.

Main Results:

Functional RNA structures are often found in non-conserved sequence regions, challenging traditional alignment-based prediction methods.
Current comparative methods primarily rely on multiple sequence alignments, which may miss structures in divergent regions.
The 'first-fold-then-align' approach shows potential but is underdeveloped.

Conclusions:

Novel computational methods are needed to improve the prediction of long-range RNA structures.
Advancements in both 'first-align-then-fold' and 'first-fold-then-align' strategies are crucial for discovering new RNA structures and interactions.
Improved methods will enhance our understanding of RNA higher-order organization and RNA-RNA interactions across the transcriptome.