Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing
Splicing is highly regulated and is modulated by numerous factors. Quantitative predictions for how a mutation will affect precursor mRNA (pre-mRNA) structure and downstream function are particularly challenging. Here, we use a novel chemical probing strategy to visualize endogenous precursor and ma...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2022-06-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/73888 |
| _version_ | 1811252693218361344 |
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| author | Jayashree Kumar Lela Lackey Justin M Waldern Abhishek Dey Anthony M Mustoe Kevin M Weeks David H Mathews Alain Laederach |
| author_facet | Jayashree Kumar Lela Lackey Justin M Waldern Abhishek Dey Anthony M Mustoe Kevin M Weeks David H Mathews Alain Laederach |
| author_sort | Jayashree Kumar |
| collection | DOAJ |
| description | Splicing is highly regulated and is modulated by numerous factors. Quantitative predictions for how a mutation will affect precursor mRNA (pre-mRNA) structure and downstream function are 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 pre-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 pre-mRNA best predicted alternative splicing outcomes for exon 10 inclusion of the alternatively spliced MAPT gene, achieving 74% accuracy. We further developed a β-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 6 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. |
| first_indexed | 2024-04-12T16:39:27Z |
| format | Article |
| id | doaj.art-7e9b5b2f330645718e814d97ac9b25a0 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T16:39:27Z |
| publishDate | 2022-06-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-7e9b5b2f330645718e814d97ac9b25a02022-12-22T03:24:52ZengeLife Sciences Publications LtdeLife2050-084X2022-06-011110.7554/eLife.73888Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probingJayashree Kumar0https://orcid.org/0000-0001-6914-748XLela Lackey1https://orcid.org/0000-0003-2163-4005Justin M Waldern2Abhishek Dey3Anthony M Mustoe4https://orcid.org/0000-0001-9346-1559Kevin M Weeks5David H Mathews6Alain Laederach7https://orcid.org/0000-0002-5088-9907Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States; Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United StatesDepartment of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States; Department of Genetics and Biochemistry, Center for Human Genetics, Clemson University, Greenwood, United StatesDepartment of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United StatesDepartment of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United StatesVerna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United StatesDepartment of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, United StatesDepartment of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, United StatesDepartment of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States; Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United StatesSplicing is highly regulated and is modulated by numerous factors. Quantitative predictions for how a mutation will affect precursor mRNA (pre-mRNA) structure and downstream function are 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 pre-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 pre-mRNA best predicted alternative splicing outcomes for exon 10 inclusion of the alternatively spliced MAPT gene, achieving 74% accuracy. We further developed a β-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 6 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.https://elifesciences.org/articles/73888alternative splicingbeta regressionRNA structural ensembleTaudisease variantschemical structure probing |
| spellingShingle | Jayashree Kumar Lela Lackey Justin M Waldern Abhishek Dey Anthony M Mustoe Kevin M Weeks David H Mathews Alain Laederach Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing eLife alternative splicing beta regression RNA structural ensemble Tau disease variants chemical structure probing |
| title | Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing |
| title_full | Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing |
| title_fullStr | Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing |
| title_full_unstemmed | Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing |
| title_short | Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing |
| title_sort | quantitative prediction of variant effects on alternative splicing in mapt using endogenous pre messenger rna structure probing |
| topic | alternative splicing beta regression RNA structural ensemble Tau disease variants chemical structure probing |
| url | https://elifesciences.org/articles/73888 |
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