Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing
Summary
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.
DRB-4SU seq of Ctrl and Mago condition in 2 replicates with fragmentation [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]
ChIP of PolII from cells with Mago knockdown, control knockdown, and RnpS1 knockdwon [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]
DAM ID sequencing of DAM fusion with Cdk9 in Control and Mago knockdown [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]
ChIP of Ser2P PolII from cells with Mago knockdown and control knockdown [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]
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