Abstract
Piwi-interacting RNAs (piRNAs) are a class of small noncoding RNAs bound to specific Argonaute proteins, the PIWI proteins. piRNAs target mRNAs by complementarity to silence them; they play an important role in the repression of transposable elements in the germ line of many species. piRNAs and PIWI proteins are also involved in diverse biological processes through their role in the regulation of cellular mRNAs. In the Drosophila embryo, they contribute to the maternal mRNA decay occurring during the maternal-to-zygotic transition. CLIP (UV cross-linking and immunoprecipitation) techniques have been used to identify target mRNAs of Argonaute proteins. Here we describe the iCLIP (individual-nucleotide resolution CLIP) protocol that we have adapted for the PIWI protein Aubergine in Drosophila embryos.