Open Access
Genes, volume 9, issue 6, pages 302
Towards Long-Range RNA Structure Prediction in Eukaryotic Genes
Pervouchine Dmitri D
1, 2, 3
Publication type: Journal Article
Publication date: 2018-06-15
PubMed ID:
29914113
Genetics
Genetics (clinical)
Abstract
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.
Citations by journals
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PeerJ
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PeerJ
1 publication, 4.17%
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Acta Naturae
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Acta Naturae, 1, 4.17%
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1 publication, 4.17%
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1 publication, 4.17%
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Citations by publishers
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Elsevier
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Elsevier
6 publications, 25%
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Oxford University Press
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Oxford University Press
4 publications, 16.67%
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Multidisciplinary Digital Publishing Institute (MDPI)
2 publications, 8.33%
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Cold Spring Harbor Laboratory
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Cold Spring Harbor Laboratory
2 publications, 8.33%
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Springer Nature
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Springer Nature
1 publication, 4.17%
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Frontiers Media S.A.
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Frontiers Media S.A.
1 publication, 4.17%
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Wiley
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Wiley
1 publication, 4.17%
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PeerJ
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PeerJ
1 publication, 4.17%
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Acta Naturae Ltd
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Acta Naturae Ltd, 1, 4.17%
Acta Naturae Ltd
1 publication, 4.17%
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- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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RIS
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TY - JOUR
DO - 10.3390/genes9060302
UR - https://doi.org/10.3390%2Fgenes9060302
TI - Towards Long-Range RNA Structure Prediction in Eukaryotic Genes
T2 - Genes
AU - Pervouchine, Dmitri D
PY - 2018
DA - 2018/06/15 00:00:00
PB - Multidisciplinary Digital Publishing Institute (MDPI)
SP - 302
IS - 6
VL - 9
PMID - 29914113
SN - 2073-4425
ER -
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@article{2018_Pervouchine,
author = {Dmitri D Pervouchine},
title = {Towards Long-Range RNA Structure Prediction in Eukaryotic Genes},
journal = {Genes},
year = {2018},
volume = {9},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
month = {jun},
url = {https://doi.org/10.3390%2Fgenes9060302},
number = {6},
pages = {302},
doi = {10.3390/genes9060302}
}
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MLA
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Pervouchine, Dmitri D., et al. “Towards Long-Range RNA Structure Prediction in Eukaryotic Genes.” Genes, vol. 9, no. 6, Jun. 2018, p. 302. https://doi.org/10.3390%2Fgenes9060302.