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. 2016 Mar 1;11(3):e0150353.
doi: 10.1371/journal.pone.0150353. eCollection 2016.

lncRNA-RNA Interactions across the Human Transcriptome

Michał Wojciech Szcześniak  1 , Izabela Makałowska  1
Affiliations

lncRNA-RNA Interactions across the Human Transcriptome

Michał Wojciech Szcześniak et al. PLoS One. .

Abstract

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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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Possible roles of lncRNA-mediated interactions in transcript processing, stability control and expression regulation.
Fig 2
Fig 2. A summary of our approach aiming at identification of regulatory lncRNA-RNA interactions.
See this image and copyright information in PMC

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