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  Global donor and acceptor splicing site kinetics in human cells.

Wachutka, L., Caizzi, L., Gagneur, J., & Cramer, P. (2019). Global donor and acceptor splicing site kinetics in human cells. eLife, 8: e45056. doi:10.7554/eLife.45056.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0003-7EFE-3 Version Permalink: http://hdl.handle.net/21.11116/0000-0003-CABE-4
Genre: Journal Article

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 Creators:
Wachutka, L., Author
Caizzi, L.1, Author              
Gagneur, J., Author
Cramer, P.1, Author              
Affiliations:
1Department of Molecular Biology, MPI for Biophysical Chemistry, Max Planck Society, ou_1863498              

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Free keywords: computational biology; genetics; genomics; human; systems biology
 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.

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Language(s): eng - English
 Dates: 2019-04-26
 Publication Status: Published online
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.7554/eLife.45056
 Degree: -

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Title: eLife
Source Genre: Journal
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Pages: 52 Volume / Issue: 8 Sequence Number: e45056 Start / End Page: - Identifier: -