Systematic Transcriptome Wide Analysis of lncRNAmiRNA Interactions
IR@IGIB: CSIR-Institute of Genomics & Integrative Biology, New Delhi
View Archive Info| Field | Value | |
| Title |
Systematic Transcriptome Wide Analysis of lncRNAmiRNA
Interactions
|
|
| Creator |
Jalali, Saakshi
Bhartiya, Deeksha Lalwani, Mukesh kumar Sivasubbu, Sridhar Scaria, Vinod |
|
| Subject |
CH1 Chemical Biology
|
|
| Description |
Abstract
Background: Long noncoding RNAs (lncRNAs) are a recently discovered class of non-protein coding RNAs, which have now
increasingly been shown to be involved in a wide variety of biological processes as regulatory molecules. The functional role
of many of the members of this class has been an enigma, except a few of them like Malat and HOTAIR. Little is known
regarding the regulatory interactions between noncoding RNA classes. Recent reports have suggested that lncRNAs could
potentially interact with other classes of non-coding RNAs including microRNAs (miRNAs) and modulate their regulatory
role through interactions. We hypothesized that lncRNAs could participate as a layer of regulatory interactions with miRNAs.
The availability of genome-scale datasets for Argonaute targets across human transcriptome has prompted us to
reconstruct a genome-scale network of interactions between miRNAs and lncRNAs.
Results: We used well characterized experimental Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation
(PAR-CLIP) datasets and the recent genome-wide annotations for lncRNAs in public domain to construct
a comprehensive transcriptome-wide map of miRNA regulatory elements. Comparative analysis revealed that in addition to
targeting protein-coding transcripts, miRNAs could also potentially target lncRNAs, thus participating in a novel layer of
regulatory interactions between noncoding RNA classes. Furthermore, we have modeled one example of miRNA-lncRNA
interaction using a zebrafish model. We have also found that the miRNA regulatory elements have a positional preference,
clustering towards the mid regions and 39 ends of the long noncoding transcripts. We also further reconstruct a genomewide
map of miRNA interactions with lncRNAs as well as messenger RNAs.
Conclusions: This analysis suggests widespread regulatory interactions between noncoding RNAs classes and suggests
a novel functional role for lncRNAs. We also present the first transcriptome scale study on miRNA-lncRNA interactions and
the first report of a genome-scale reconstruction of a noncoding RNA regulatory interactome involving lncRNAs.
Citation: Jalali S, Bhartiya D, Lalwani MK, Sivasubbu S, Scaria V (2013) Systematic Transcriptome Wide Analysis of lncRNA-miRNA Interactions. PLoS ONE 8(2):
e53823. doi:10.1371/journal.pone.0053823
Editor: Lin Zhang, University of Pennsylvania School of Medicine, United States of America
Received February 27, 2012; Accepted December 6, 2012; Published February 6, 2013
Copyright: � 2013 Jalali et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: The authors acknowledge funding from the Council of Scientific and Industrial Research (CSIR), India through the NWP0036 and FAC002 Grants. The
funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing Interests: The authors have declared that no competing interests exist.
E-mail: vinods@igib.res.in (VS); s.sivasubbu@igib.res.in (SS)
These authors contributed equally to this work.
|
|
| Date |
2013-02
|
|
| Type |
Article
PeerReviewed |
|
| Format |
application/pdf
|
|
| Identifier |
http://openaccess.igib.res.in/156/1/Jalali%20et%20al%202013.pdf
Jalali, Saakshi and Bhartiya, Deeksha and Lalwani, Mukesh kumar and Sivasubbu, Sridhar and Scaria, Vinod (2013) Systematic Transcriptome Wide Analysis of lncRNAmiRNA Interactions. Systematic Transcriptome Wide Analysis of lncRNAmiRNA Interactions, 8 (2). |
|
| Relation |
http://openaccess.igib.res.in/156/
|
|