Identifying trypanosome protein-RNA interactions using RIP-Seq

Abstract

Trypanosomatids rely primarily on post-transcriptional mechanisms for the control of gene expression, with regulation of RNA processing, localization, degradation and translation by RNA-binding proteins (RBPs). To determine the mechanisms by which RBPs control gene expression in trypanosomatids, transcriptome-wide identification of mRNA targets and mapping of the RNA-binding site is required. Here we present our most current RIP-Seq (RNA immunoprecipitation followed by high-throughput sequencing) protocol that we generally apply to elucidate RNA/protein interaction in Trypanosoma brucei. The technique provides valuable information about the workings of messenger ribonucleoprotein (mRNP ) networks and trypanosome gene expression mechanisms.