Tools for Experimental and Computational Genome-Wide Analysis of the Function of DDX5 and DDX17 Helicases in RNA Processing.

DEAD-box helicases DDX5 and DDX17 play a key role in regulating gene expression and RNA processing in mammalian cells. In particular, they are involved in alternative splicing and in the 3' end processing of nascent transcripts associated with the termination of transcription. In this chapter, we present experimental protocols and computational tools that altogether enable the prediction and validation of various types of changes in the neuroblastoma cell transcriptome upon the depletion of both helicases. This includes protocols for monitoring variations in alternative splicing, readthrough transcription resulting from defects in 3' end processing, and the production of fusion transcripts associated with readthrough.