Abstract
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.
Highlights
Promoter-proximal pausing of RNA polymerase II (Pol II) is a widespread transcriptional regulatory step across metazoans
Genetically increasing Pol II pausing rescues exon skipping events and the eye phenotype associated with KD of pre-exon junction complex (EJC) components, indicating that restraining Pol II release into gene bodies is sufficient to complement the loss of pre-EJC components in exon definition
Our work uncovers an unexpected connection between the nuclear EJC and the transcription machinery via the regulation of Pol II pausing, which is conserved from flies to human
Summary
Promoter-proximal pausing of RNA polymerase II (Pol II) is a widespread transcriptional regulatory step across metazoans. 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. We observed that depletion of pre-EJC components, but not of the EJC splicing subunit RnpS1, lead to a global decrease in promoter proximal pausing, altered Pol II phosphorylation state and premature entry into elongation. These changes are concomitant with underlying changes in chromatin architecture and correlate strongly with exon skipping events. Our results demonstrate a direct role of the pre-EJC in exon definition via the control of promoter proximal pausing
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