DRB-4SU seq of Ctrl and Mago condition in 2 replicates with fragmentation [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]. DRB-4SU seq of Ctrl and Mago condition in 2 replicates with fragmentation [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]

Promoter-proximal pausing of RNA polymerase II (Pol II) is a widespread transcriptional regulatory step across metazoans. Here we find that the nuclear exon junction complex (pre-EJC) is a critical and conserved regulator of this process. Depletion of pre-EJC subunits leads to a global decrease in Pol II pausing and to premature entry into elongation. This effect occurs, at least in part, via non-canonical recruitment of pre-EJC components at promoters. Failure to recruit the pre-EJC at promoters results in increased binding of the positive transcription elongation complex (P-TEFb) and in enhanced Pol II release. Notably, restoring pausing is sufficient to rescue exon skipping and the photoreceptor differentiation defect associated with depletion of pre-EJC components in vivo. We propose that the pre-EJC serves as an early transcriptional checkpoint to prevent premature entry into elongation, ensuring proper recruitment of RNA processing components that are necessary for exon definition. Overall design: DRB-4SU seq of Ctrl and Mago condition in 2 replicates. The 4SU labelling was perofromed for 6 minutes. During the enrichment of the biotinylated RNA on streptavidin beads, the RNA was digested with RNAse T1 to > 100bp to improve the resolution.