Establishing a method for RNA immunoprecipitation to study interactions between long non-coding RNAs and proteins

Abstract

Long non-coding RNAs (lncRNAs) are involved in several important biological processes, and several lncRNAs have been associated with human diseases, particularly cancer. LncRNAs regulate gene expression at different levels. LncRNAs exert their functions through interactions with DNA, RNA or proteins. In this study, we established a method for investigating interactions between lncRNAs and protein complexes in human breast cancer cell lines. We used the well-known interaction between HOTAIR and the PRC2 member Suz12 to work out a RNA immunoprecipitation protocol in the lab, using an antibody targeting Suz12 to co-immunoprecipitate HOTAIR from nuclear lysates from the Hs578 breast cancer cells. We achieved a significant enrichment of HOTAIR in the immunoprecipitate from nuclear extracts from Hs578T. Differential expression of HOTAIR in the three breast cancer cell lines Hs578T, MDA-MB-231 and MCF-7 were also observed.