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lncRNA-RNA Interactions across the Human Transcriptome

Long non-coding RNAs (lncRNAs) represent a numerous class of non-protein coding transcripts longer than 200 nucleotides. There is possibility that a fraction of lncRNAs are not functional and represent mere transcriptional noise but a growing body of evidence shows they are engaged in a plethora of...

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Detalles Bibliográficos
Autores principales: Szcześniak, Michał Wojciech, Makałowska, Izabela
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4773119/
https://www.ncbi.nlm.nih.gov/pubmed/26930590
http://dx.doi.org/10.1371/journal.pone.0150353
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author Szcześniak, Michał Wojciech
Makałowska, Izabela
author_facet Szcześniak, Michał Wojciech
Makałowska, Izabela
author_sort Szcześniak, Michał Wojciech
collection PubMed
description Long non-coding RNAs (lncRNAs) represent a numerous class of non-protein coding transcripts longer than 200 nucleotides. There is possibility that a fraction of lncRNAs are not functional and represent mere transcriptional noise but a growing body of evidence shows they are engaged in a plethora of molecular functions and contribute considerably to the observed diversification of eukaryotic transcriptomes and proteomes. Still, however, only ca. 1% of lncRNAs have well established functions and much remains to be done towards decipherment of their biological roles. One of the least studied aspects of lncRNAs biology is their engagement in gene expression regulation through RNA-RNA interactions. By hybridizing with mate RNA molecules, lncRNAs could potentially participate in modulation of pre-mRNA splicing, RNA editing, mRNA stability control, translation activation, or abrogation of miRNA-induced repression. Here, we implemented a similarity-search based method for transcriptome-wide identification of RNA-RNA interactions, which enabled us to find 18,871,097 lncRNA-RNA base-pairings in human. Further analyses showed that the interactions could be involved in processing, stability control and functions of 57,303 transcripts. An extensive use of RNA-Seq data provided support for approximately one third of the interactions, at least in terms of the two RNA components being co-expressed. The results suggest that lncRNA-RNA interactions are broadly used to regulate and diversify the human transcriptome.
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spelling pubmed-47731192016-03-07 lncRNA-RNA Interactions across the Human Transcriptome Szcześniak, Michał Wojciech Makałowska, Izabela PLoS One Research Article Long non-coding RNAs (lncRNAs) represent a numerous class of non-protein coding transcripts longer than 200 nucleotides. There is possibility that a fraction of lncRNAs are not functional and represent mere transcriptional noise but a growing body of evidence shows they are engaged in a plethora of molecular functions and contribute considerably to the observed diversification of eukaryotic transcriptomes and proteomes. Still, however, only ca. 1% of lncRNAs have well established functions and much remains to be done towards decipherment of their biological roles. One of the least studied aspects of lncRNAs biology is their engagement in gene expression regulation through RNA-RNA interactions. By hybridizing with mate RNA molecules, lncRNAs could potentially participate in modulation of pre-mRNA splicing, RNA editing, mRNA stability control, translation activation, or abrogation of miRNA-induced repression. Here, we implemented a similarity-search based method for transcriptome-wide identification of RNA-RNA interactions, which enabled us to find 18,871,097 lncRNA-RNA base-pairings in human. Further analyses showed that the interactions could be involved in processing, stability control and functions of 57,303 transcripts. An extensive use of RNA-Seq data provided support for approximately one third of the interactions, at least in terms of the two RNA components being co-expressed. The results suggest that lncRNA-RNA interactions are broadly used to regulate and diversify the human transcriptome. Public Library of Science 2016-03-01 /pmc/articles/PMC4773119/ /pubmed/26930590 http://dx.doi.org/10.1371/journal.pone.0150353 Text en © 2016 Szcześniak, Makałowska http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Szcześniak, Michał Wojciech
Makałowska, Izabela
lncRNA-RNA Interactions across the Human Transcriptome
title lncRNA-RNA Interactions across the Human Transcriptome
title_full lncRNA-RNA Interactions across the Human Transcriptome
title_fullStr lncRNA-RNA Interactions across the Human Transcriptome
title_full_unstemmed lncRNA-RNA Interactions across the Human Transcriptome
title_short lncRNA-RNA Interactions across the Human Transcriptome
title_sort lncrna-rna interactions across the human transcriptome
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4773119/
https://www.ncbi.nlm.nih.gov/pubmed/26930590
http://dx.doi.org/10.1371/journal.pone.0150353
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