Systematic transcriptome wide analysis of lncRNA-miRNA interactions.

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Long noncoding RNAs (lncRNAs) are regulatory molecules with largely unknown functions.
• Interactions between lncRNAs and microRNAs (miRNAs) are poorly understood.
• Recent advances allow for genome-scale investigation of noncoding RNA interactions.

Purpose of the Study:

• To reconstruct a genome-scale network of interactions between miRNAs and lncRNAs.
• To investigate the regulatory role of lncRNAs in conjunction with miRNAs.
• To explore a novel layer of regulatory interactions between noncoding RNA classes.

Main Methods:

• Utilized Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) datasets.
• Employed genome-wide annotations for lncRNAs.
• Constructed a transcriptome-wide map of miRNA regulatory elements and interactions.

Main Results:

• Demonstrated that miRNAs can target lncRNAs, in addition to protein-coding transcripts.
• Identified positional preferences for miRNA regulatory elements on lncRNAs.
• Modeled a specific miRNA-lncRNA interaction in a zebrafish model.
• Reconstructed a genome-wide map of miRNA interactions with both lncRNAs and messenger RNAs.

Conclusions:

• Suggests widespread regulatory interactions between noncoding RNA classes.
• Proposes a novel functional role for lncRNAs in gene regulation.
• Presents the first transcriptome-scale study of miRNA-lncRNA interactions and a genome-scale noncoding RNA interactome.