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Towards Long-Range RNA Structure Prediction in Eukaryotic Genes

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 l...

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Autor principal: Pervouchine, Dmitri D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6027157/
https://www.ncbi.nlm.nih.gov/pubmed/29914113
http://dx.doi.org/10.3390/genes9060302
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author Pervouchine, Dmitri D.
author_facet Pervouchine, Dmitri D.
author_sort Pervouchine, Dmitri D.
collection PubMed
description 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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spelling pubmed-60271572018-07-13 Towards Long-Range RNA Structure Prediction in Eukaryotic Genes Pervouchine, Dmitri D. Genes (Basel) Review 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. MDPI 2018-06-15 /pmc/articles/PMC6027157/ /pubmed/29914113 http://dx.doi.org/10.3390/genes9060302 Text en © 2018 by the author. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Review
Pervouchine, Dmitri D.
Towards Long-Range RNA Structure Prediction in Eukaryotic Genes
title Towards Long-Range RNA Structure Prediction in Eukaryotic Genes
title_full Towards Long-Range RNA Structure Prediction in Eukaryotic Genes
title_fullStr Towards Long-Range RNA Structure Prediction in Eukaryotic Genes
title_full_unstemmed Towards Long-Range RNA Structure Prediction in Eukaryotic Genes
title_short Towards Long-Range RNA Structure Prediction in Eukaryotic Genes
title_sort towards long-range rna structure prediction in eukaryotic genes
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6027157/
https://www.ncbi.nlm.nih.gov/pubmed/29914113
http://dx.doi.org/10.3390/genes9060302
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