Significant enrichment of RNA binding protein sites across some lncRNA classes

Long non-coding RNAs (lncRNAs), are being reported to be extensively involved in diverse regulatory roles and have exhibited numerous disease associations. LncRNAs modulate their function through interaction with other biomolecules in the cell including DNA, RNA, and proteins. The availability of genome-scale experimental datasets of RNA binding proteins (RBP) motivated us to understand the role of lncRNAs in terms of its interactions with these proteins. Researchers from CSIR Institute of Genomics and Integrative Biology demonstrate a comprehensive study of interactions between RBP and lncRNAs at a transcriptome scale through extensive analysis of the crosslinking and immunoprecipitation (CLIP) experimental datasets available for 70 RNA binding proteins.

Their analysis suggests that density of interaction sites for these proteins was significantly higher for specific sub-classes of lncRNAs when compared to protein-coding transcripts. They also observed a positional preference of these RBPs across lncRNA and protein coding transcripts in addition to a significant co-occurrence of RBPs having similar functions, suggesting a modular organization of these elements across lncRNAs.


Depiction of the mapping of RNA binding protein interaction sites from CLIPdb-CIMS, CLIPdb-CITS, and CLIPdb-Piranha-stranded datasets across the length of MALAT1 lncRNA. The RBP highlighted in gray box are the ones generally localized to cytoplasm (C). The RBP generally localized to nucleus (N) are marked as yellow box. C/N labeled RBPs is the ones which are present in both Nucleus and Cytoplasm.

The significant enrichment of RBP sites across some lncRNA classes is suggestive that these interactions might be important in understanding the functional role of lncRNA. These researchers observed a significant enrichment of RBPs which are involved in functional roles such as silencing, splicing, mRNA processing, and transport, indicating the potential participation of lncRNAs in such processes.

Jalali S, Gandhi S, Scaria V. (2018) Distinct and Modular Organization of Protein Interacting Sites in Long Non-coding RNAs. Front Mol Biosci 5:27. [article]

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