TY - JOUR TI - Global donor and acceptor splicing site kinetics in human cells AU - Wachutka, Leonhard AU - Caizzi, Livia AU - Gagneur, Julien AU - Cramer, Patrick A2 - Black, Douglas L A2 - Manley, James L VL - 8 PY - 2019 DA - 2019/04/26 SP - e45056 C1 - eLife 2019;8:e45056 DO - 10.7554/eLife.45056 UR - https://doi.org/10.7554/eLife.45056 AB - RNA splicing is an essential part of eukaryotic gene expression. Although the mechanism of splicing has been extensively studied in vitro, in vivo kinetics for the two-step splicing reaction remain poorly understood. Here, we combine transient transcriptome sequencing (TT-seq) and mathematical modeling to quantify RNA metabolic rates at donor and acceptor splice sites across the human genome. Splicing occurs in the range of minutes and is limited by the speed of RNA polymerase elongation. Splicing kinetics strongly depends on the position and nature of nucleotides flanking splice sites, and on structural interactions between unspliced RNA and small nuclear RNAs in spliceosomal intermediates. Finally, we introduce the ‘yield’ of splicing as the efficiency of converting unspliced to spliced RNA and show that it is highest for mRNAs and independent of splicing kinetics. These results lead to quantitative models describing how splicing rates and yield are encoded in the human genome. KW - co-transcriptional splicing KW - splicing kinetic KW - RNA metabolism KW - metabolic labeling KW - gene regulatory elements KW - splicing yield JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -