RNA binding proteins (RBPs) are vital enzymes for proper function of RNA regulatory pathways that range from chromatin packaging to mRNA translation. When RBPs and RNA interact, they form highly dynamic ribonucleoprotein (RNP) complexes, often in a combinatorial fashion. RNA-protein interactions are dependent on the RNA structure, which however is largely unreadable from the sequence content alone. Therefore, the binding and processing capacities of these protein partners remain poorly explored on the transcriptome-wide level. We are investigating the regulatory mechanisms of mammalian RBPs in noncoding and coding RNA processing by developing a new approach (called RAP-seq) to identify the binding patterns of RBPs. By using an exhaustive and unbiased transcriptome-wide approach in human and mouse cell lines, we aim to identify the RNA binding motifs and their degree of conservation. Our long-term aim is to construct transcriptional networks governed by RBPs.