Guidelines to Study Transcriptome Remodeling by Proteins Using Deep Sequencing (RNA-Seq)

RNA remodeling proteins (RRPs) are key regulators of RNA metabolism, often exerting broad, pleiotropic effects on the cellular transcriptome. Deep RNA sequencing (RNA-seq) has become a standard approach for investigating these effects on a global scale, particularly for identifying patterns of differential gene expression or splicing associated with RRP activity. In this chapter, we outline best-practice guidelines for designing and executing RNA-seq experiments, integrating bench and computational steps into a rigorous workflow. Data generated through this process provide a strong foundation for deploying other advanced approaches such as CLIP-seq or SHAPE-seq to uncover RRP targets, elucidate RRP functions, or detect RNA structural changes at global scale.