Isolation of protein complexes associated with long noncoding RNAs

Abstract

Long noncoding RNAs (lncRNAs) are a new class of regulatory genes that play critical roles in various processes ranging from normal development to human diseases. Recent studies have shown that protein complexes are required for the functions of lncRNAs. The identification of these proteins which are associated with lncRNAs is critical for the understanding of molecular mechanisms of lncRNAs in gene regulation and their functions. In this chapter, we describe a method to isolate proteins associated with lncRNAs. This procedure involves fusion protein maltose-binding protein (MBP) fused to MS2-binding protein to pull down the proteins associated with lncRNA and the identification of these proteins by mass spectrometry.