Global donor and acceptor splicing site kinetics in human cells

Abstract
Data availability
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Abstract

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.

Data availability

The sequencing data and processed files were deposited in NCBI Gene Expression Omnibus (GEO) database under accession code GSE129635.

The following data sets were generated

(2019) Global donor and acceptor splicing site kinetics in human cells
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https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129635

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Article and author information

Author details

Leonhard Wachutka

Department of Informatics, Technical University of Munich, Garching, Germany

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-5959-040X
Livia Caizzi

Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-9723-6893
Julien Gagneur

Department of Informatics, Technical University of Munich, Garching, Germany

For correspondence
gagneur@in.tum.de

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-8924-8365
Patrick Cramer

Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany

For correspondence
patrick.cramer@mpibpc.mpg.de

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-5454-7755

Funding

European Molecular Biology Organization (ALTF-1261-2014)

Livia Caizzi

Horizon 2020 SOUND (633974)

Leonhard Wachutka
Julien Gagneur

European Research Council

Patrick Cramer

Volkswagen Foundation

Patrick Cramer

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

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.