Biochemical analysis of long non-coding RNA-containing ribonucleoprotein complexes

Long non-coding RNAs (IncRNAs), once relegated to junk products of the genome, are becoming better appreciated for the myriad functions they play in cellular processes. It is clear that for most of the cases studied, IncRNAs carry out their functions at least in part through interactions with proteins. Here we present two complementary biochemical methods for the analysis of IncRNA-containing ribonucleoprotein complexes, hereafter referred to as RNPs. The first strategy offers users the ability to purify RNPs based on a protein component and to analyze the spectrum of IncRNAs, other proteins, and, if present, other types of RNAs that are bound to it. The second makes use of a bacteriophage MS2 binding-site affinity-handle grafted onto an IncRNA of interest to investigate the proteins and RNAs that co-purify with the tagged RNA. (C) 2012 Elsevier Inc. All rights reserved.