Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing
- University of North Carolina at Chapel Hill, United States
- Clemson University, United States
- Baylor College of Medicine, United States
- University of Rochester, United States
Abstract
Splicing is highly regulated and is modulated by numerous factors. Quantitative predictions for how a mutation will affect precursor messenger RNA (mRNA) structure and downstream function is particularly challenging. Here we use a novel chemical probing strategy to visualize endogenous precursor and mature MAPT mRNA structures in cells. We used these data to estimate Boltzmann suboptimal structural ensembles, which were then analyzed to predict consequences of mutations on precursor mRNA structure. Further analysis of recent cryo-EM structures of the spliceosome at different stages of the splicing cycle revealed that the footprint of the Bact complex with precursor mRNA best predicted alternative splicing outcomes for exon 10 inclusion of the alternatively spliced MAPT gene, achieving 74% accuracy. We further developed a b-regression weighting framework that incorporates splice site strength, RNA structure, and exonic/intronic splicing regulatory elements capable of predicting, with 90% accuracy, the effects of 47 known and six newly discovered mutations on inclusion of exon 10 of MAPT. This combined experimental and computational framework represents a path forward for accurate prediction of splicing-related disease-causing variants.
Data availability
Sequencing data have been deposited in SRA under BioProject ID PRJNA762079 and PRJNA812003.DMS Reactivities are available as SNRNASMs at https://bit.ly/2WaDw6FAll data generated or analyzed during this study are included in the manuscript and supporting files; Source Data files have been provided for Figures 1,2,4,5 and 6.Modeling and feature generation code is uploaded at https://git.io/JuSW8
Article and author information
Author details
Funding
National Institutes of Health (R01 HL111527)
- Alain Laederach
National Institutes of Health (R35 GM 140844)
- Alain Laederach
National Institutes of Health (R01 GM076485)
- David H Mathews
National Institutes of Health (R35 GM122532)
- Kevin Weeks
Cancer Prevention and Research Institute of Texas (CPRIT Scholar)
- Anthony M Mustoe
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, Kumar 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.
Metrics
-
- 1,979
- views
-
- 448
- downloads
-
- 8
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing
eLife 11:e73888.
https://doi.org/10.7554/eLife.73888
Further reading
-
- Computational and Systems Biology
- Medicine
Sudden death after myocardial infarction (MI) is associated with electrophysiological heterogeneities and ionic current remodelling. Low ejection fraction (EF) is used in risk stratification, but its mechanistic links with pro-arrhythmic heterogeneities are unknown. We aim to provide mechanistic explanations of clinical phenotypes in acute and chronic MI, from ionic current remodelling to ECG and EF, using human electromechanical modelling and simulation to augment experimental and clinical investigations. A human ventricular electromechanical modelling and simulation framework is constructed and validated with rich experimental and clinical datasets, incorporating varying degrees of ionic current remodelling as reported in literature. In acute MI, T-wave inversion and Brugada phenocopy were explained by conduction abnormality and local action potential prolongation in the border zone. In chronic MI, upright tall T-waves highlight large repolarisation dispersion between the border and remote zones, which promoted ectopic propagation at fast pacing. Post-MI EF at resting heart rate was not sensitive to the extent of repolarisation heterogeneity and the risk of repolarisation abnormalities at fast pacing. T-wave and QT abnormalities are better indicators of repolarisation heterogeneities than EF in post-MI.
-
- Computational and Systems Biology
Measuring mitochondrial respiration in frozen tissue samples provides the first comprehensive atlas of how aging affects mitochondrial function in mice.
