Cross-linking immunoprecipitation followed by sequencing (CLIP-seq) is a family of methods for profiling sites of protein binding to RNA. In particular, CLIP has been used to identify targets of microRNAs, small non-coding RNA molecules that bind to a protein Ago2 and thus regulate gene expression post-transcriptionally. We developed a new algorithm CLIPanalyze for analysis of such data and used it for comprehensive analysis of microRNA targets in vivo in mouse embryonic stem cells, developing embryos, adult tissues and multiple cancer models. We now continue development and application of methods for studies of post-transcriptional regulation.