Transcription and splicing kinetics are coordinated within both genes and higher-order chromatin domains [dataset1]

Here, we set out to understand if and how splicing kinetics are coordinated beyond individual intron removal and if this potential coordination could regulate alternative splicing outcomes. By measuring rates of transcription and splicing genome-wide, we found that the rate of splicing is coordinated across introns within individual genes. Furthermore, we found that elongation rates and splicing rates are coordinated within TADs, as are alternative splicing changes that result from cell type differences, differentiation programs, and alterations in splicing factor levels. Overall, our work establishes that the kinetics of transcription and splicing are coordinated within the spatial organization of the genome, which could be a control point for alternative splicing regulation that can modulate the function of a cell. Nascent RNA-sequencing in two cell lines at 7 time points following 3hr DRB treatment and washout Please note that the *_steadyState samples represent those treated with DMSO as a vehicle control for 3 hours.