Profiling of Brat associated mRNAs from Drosophila embryos by RIP-CHIP

The Drosophila TRIM-NHL protein Brain tumor (Brat) plays important roles during early embryogenesis, in cell fate decisions, during neurogenesis and in mature neurons. Brat is an RNA-binding protein and functions as translational repressor. However, which RNAs Brat regulates and how RNA-binding specificity is achieved, is unknown. Using RNA-Immunoprecipitation we identify Brat-bound mRNAs in Drosophila embryos and define a consensus binding motif. Microarrays were used to profile Brat-associated RNAs from fly embryos. Flag-myc-Brat was precipitated from Drosophila embryo lysates and bound RNAs were profiled using microarrays. Precipitation from wild type flies served as negative control.