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.
Highlights
An explosion of microarray tiling and highthroughput deep sequencing analysis has led to the discovery of thousands of previously presumed non-coding transcripts [1, 2]
Characteristics and function of long non-coding RNA (lncRNA) LncRNA are a group of non-coding RNAs defined as being larger than 200 nucleotides in length, which distinguish them from small RNAs such as microRNAs, small nucleolar RNAs and small interfering RNAs [11]
To developed a highthroughput method to identify proteins associated with a specific lncRNA in vivo, McHugh and colleagues combined RNA antisense purification (RAP) with mass spectrometry (MS) to obtain high yields of RNA complex and identified ten proteins associated with lncRNA Xist, including SHARP, RBM15, MYEF2, CELF1, HNRNPC, Fig. 2 Schematic representation of chromatin isolation by RNA purification (ChIRP), capture hybridization analysis of RNA targets (CHART) and RAP to identify associated proteins and chromatin DNA
Summary
An explosion of microarray tiling and highthroughput deep sequencing analysis has led to the discovery of thousands of previously presumed non-coding transcripts [1, 2]. LncRNAs, through interactions with protein, DNA and RNA, regulate gene expression at multiple levels, including chromatin remodeling and nuclear transcription,. An lncRNA induced by DNA damage and transcribed from the cyclin D1 gene promoter, recruits and integrates RNA binding protein TLS to silence cyclin D1 gene expression [22]. The 3′-end of HOTAIR associates with LSD1, inducing H3K4 demethylated modification [37] Another nascent antisense lncRNA, ANRIL, which is transcribed by RNA polymerase II at the TSS of the p16INK4a gene, recruits PRC2 and PRC1 to mediate protein-coding gene repression in cis [38]. Most methods to study RNA–protein interactions are protein-centric, including native RNA immunoprecipitation (nRIP), cross-linking and immunoprecipitation (CLIP) [43, 44].
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