Unveiling the hidden function of long non-coding RNA by identifying its major partner-protein

Abstract

Tens of thousands of long non-coding RNAs (lncRNAs) have been discovered in eukarya, but their functions are largely unknown. Fortunately, lncRNA-protein interactions may offer details of how lncRNAs play important roles in various biological processes, thus identifying proteins associated with lncRNA is critical. Here we review progress of molecular archetypes that lncRNAs execute as guides, scaffolds, or decoys for protein, focusing on advantages, shortcomings and applications of various conventional and emerging technologies to probe lncRNAs and protein interactions, including protein-centric biochemistry approaches such as nRIP and CLIP, and RNA-centric biochemistry approaches such as ChIRP, CHART and RAP. Overall, this review provides strategies for probing interactions between lncRNAs and protein.

Keywords: Biochemistry approaches; Function; Interaction; Long non-coding RNA; Protein.

Fig. 1

Schematic illustration of possible molecular archetypes of lncRNA–protein. a lncRNA guides protein to target genomic loci or the protein acts as an adaptor for lncRNA to link lncRNA to the target gene. b lncRNA brings two or three proteins together to form discrete complexes of lncRNA–RNPs. c lncRNA act as decoys to draw proteins away from t target genes

Fig. 2

Schematic representation of ChIRP, CHART and RAP to identify associated proteins and chromatin DNA. RNA–protein–DNA complexes were cross-linked in vivo and solubilized by sonication. Corresponding biotinylated oligonucleotides of three methods were designed and synthesized to be hybridized to target lncRNAs under stringent conditions. Associated proteins and chromatin DNA were efficiently pulled down with streptavidin magnetic beads. Co-purified RNA, protein and DNA were isolated with RNase elution and subjected analyzed downstream analysis. Isolated proteins were analyzed by mass spectrometry or Western blotting and chromatin DNA was used for q-PCR, deep sequencing