Coupling of Transcription with mRNA Processing in time and Space

Abstract

The cellular transcription and mRNA processing machineries appear to have co-evolved to allow coupling of the reactions they perform in space and time. Coupling in space is achieved by “recruitment” of processing factors to the nascent transcript, often by binding to the pol II CTD. Much less is known about how coupling in time is achieved, that is to say the coordination of rates of elongation and processing. Slow elongation is predicted to lengthen the window of opportunity for an event to occur at an upstream site on the nascent transcript before it must compete with an RNA sequence element further downstream. Consistent with this prediction, in a few cases slow elongation is associated with enhanced inclusion of alternative exons (ref. 1) through processing at upstream splice sites and processing at upstream alternative poly(A) sites (ref. 2). We investigated kinetic coupling in human cell lines that express pol II large subunits with mutations in funnel and trigger loop domains that slow down and speed up elongation rates genome-wide. Slow and fast elongation affected constitutive and alternative splicing, frequently altering exon inclusion and intron retention in ways not predicted by the “window of opportunity” model. Unexpectedly, slow and fast elongation often both increased or both decreased inclusion of a particular exon or retained intron. Together our results suggest that an optimal rate of transcriptional elongation is required for normal co-transcriptional pre-mRNA splicing.