Global donor and acceptor splicing site kinetics in human cells
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 model...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2019-04-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/45056 |
| _version_ | 1811199501926400000 |
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| author | Leonhard Wachutka Livia Caizzi Julien Gagneur Patrick Cramer |
| author_facet | Leonhard Wachutka Livia Caizzi Julien Gagneur Patrick Cramer |
| author_sort | Leonhard Wachutka |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T01:49:09Z |
| format | Article |
| id | doaj.art-30692b75cc824b83bf3d9429a5992660 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T01:49:09Z |
| publishDate | 2019-04-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-30692b75cc824b83bf3d9429a59926602022-12-22T03:52:58ZengeLife Sciences Publications LtdeLife2050-084X2019-04-01810.7554/eLife.45056Global donor and acceptor splicing site kinetics in human cellsLeonhard Wachutka0https://orcid.org/0000-0002-5959-040XLivia Caizzi1https://orcid.org/0000-0001-9723-6893Julien Gagneur2https://orcid.org/0000-0002-8924-8365Patrick Cramer3https://orcid.org/0000-0001-5454-7755Department of Informatics, Technical University of Munich, Garching, GermanyDepartment of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, GermanyDepartment of Informatics, Technical University of Munich, Garching, GermanyDepartment of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, GermanyRNA 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.https://elifesciences.org/articles/45056co-transcriptional splicingsplicing kineticRNA metabolismmetabolic labelinggene regulatory elementssplicing yield |
| spellingShingle | Leonhard Wachutka Livia Caizzi Julien Gagneur Patrick Cramer Global donor and acceptor splicing site kinetics in human cells eLife co-transcriptional splicing splicing kinetic RNA metabolism metabolic labeling gene regulatory elements splicing yield |
| title | Global donor and acceptor splicing site kinetics in human cells |
| title_full | Global donor and acceptor splicing site kinetics in human cells |
| title_fullStr | Global donor and acceptor splicing site kinetics in human cells |
| title_full_unstemmed | Global donor and acceptor splicing site kinetics in human cells |
| title_short | Global donor and acceptor splicing site kinetics in human cells |
| title_sort | global donor and acceptor splicing site kinetics in human cells |
| topic | co-transcriptional splicing splicing kinetic RNA metabolism metabolic labeling gene regulatory elements splicing yield |
| url | https://elifesciences.org/articles/45056 |
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