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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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Formato: | Online Artículo Texto |
Lenguaje: | English |
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MDPI
2018
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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. |
format | Online Article Text |
id | pubmed-6027157 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT pervouchinedmitrid towardslongrangernastructurepredictionineukaryoticgenes |