Three distinct velocities of elongating RNA polymerase define exons and introns

Differential elongation rates of RNA polymerase II (RNAP) have been posited to be a critical determinant for pre-mRNA splicing. Molecular dissection of mechanisms coupling transcription elongation rate with splicing requires knowledge of instantaneous RNAP elongation velocity at exon and introns. However, only average RNAP elongation rates over large genomic distances can be inferred with current approaches, and local instantaneous velocities of the elongating RNA polymerase across endogenous genomic regions remain difficult to determine at sufficient resolution to enable detailed kinetic analysis of RNAP at exons. In order to overcome these challenges and to investigate kinetic features of RNAP elongation at genomic scale, we have employed global nuclear run-on sequencing (GRO-seq) method to infer changes in local RNAP elongation rates across the human genome, as changes in the residence time of RNAP. Using this approach, we have investigated functional coupling between the changes in local pattern of RNAP elongation rate at the exons and their general expression level, as inferred by sequencing of mRNAs (mRNA-seq). Our genomic level analyses reveal acceleration of RNAP at lowly expressed exons and confirm the previously reported deceleration of RNAP at highly expressed exons, suggesting variable local velocities of elongating RNAP that are potentially associated with different inclusion or exclusion rates of exons across the human genome.\n\nAUTHOR SUMMARYUnderstanding the mechanisms that enable high precision recognition and splicing of exons is fundamental to many aspects of human development and disease. Emerging data suggest that the speed of the elongating RNA polymerase affects pre-mRNA splicing; however, systematic genomic investigation of RNAP elongation speed and pre-mRNA have been lacking. Using a recently developed method for detecting synthesized nascent RNAs, we have inferred variable elongation rates of RNA polymerase II (RNAP) that are associated with included exons, introns and excluded exons, across the human genome. From this analysis, we have identified acceleration of RNAP at exons as a major determinant of exon exclusion across the genome, while confirming previous studies showing deceleration of RNAP at included exons.