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 are encoded in the human genome.
The sequencing data and processed files were deposited in NCBI Gene Expression Omnibus (GEO) database under accession code GSE129635.
Global donor and acceptor splicing site kinetics in human cellsNCBI Gene Expression Omnibus, GSE129635.
TT-seq maps the human transient transcriptomeNCBI Gene Expression Omnibus, GSE75792.
Genome-wide discovery of human splicing branchpointsNCBI Gene Expression Omnibus, GSE53328.
Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for ActivationRCSB Protein Data Bank, 5O9Z.
An Atomic Structure of the Human SpliceosomeRCSB Protein Data Bank, 5XJC.
- Livia Caizzi
- Leonhard Wachutka
- Julien Gagneur
- Patrick Cramer
- Patrick Cramer
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
- Douglas L Black, University of California, Los Angeles, United States
© 2019, Wachutka et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.