Approaches for Dissecting RNA-Binding Protein Networks

Abstract

RNA-binding proteins (RBPs) play pivotal roles in post-transcriptional regulation, acting as master controllers of the RNA’s life. The development of a variety of global analysis tools during the last decade has tremendously enriched our understanding of the function of RBPs and their implications in environmental and cellular cues. In this chapter, we discuss the properties and functions of the RBPs in fungi, and we outline the genome-wide approaches that have been developed during the last decade to systematically identify their RNA targets. We further sketch recent approaches aimed to search for novel RBPs, revealing that many more proteins such as metabolic enzymes could have additional functions in RNA regulation. Based on a rich dataset obtained in budding yeast, we further refer to attempts to integrate RNA targets for more than 60 RBPs into molecular networks to reveal structures and motifs. Finally, we elaborate on the future tasks and challenges on our way to complete our understanding of this highly connected and interwoven protein-RNA interaction network and its importance for cell physiology