Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Kumar, Jayashree, Lackey, Lela, Waldern, Justin M, Dey, Abhishek, Mustoe, Anthony M, Weeks, Kevin M, Mathews, David H, Laederach, Alain
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9236610/
https://www.ncbi.nlm.nih.gov/pubmed/35695373
http://dx.doi.org/10.7554/eLife.73888
_version_ 1784736569877331968
author Kumar, Jayashree
Lackey, Lela
Waldern, Justin M
Dey, Abhishek
Mustoe, Anthony M
Weeks, Kevin M
Mathews, David H
Laederach, Alain
author_facet Kumar, Jayashree
Lackey, Lela
Waldern, Justin M
Dey, Abhishek
Mustoe, Anthony M
Weeks, Kevin M
Mathews, David H
Laederach, Alain
author_sort Kumar, Jayashree
collection PubMed
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 B(act) 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.
format Online
Article
Text
id pubmed-9236610
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher eLife Sciences Publications, Ltd
record_format MEDLINE/PubMed
spelling pubmed-92366102022-06-28 Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing Kumar, Jayashree Lackey, Lela Waldern, Justin M Dey, Abhishek Mustoe, Anthony M Weeks, Kevin M Mathews, David H Laederach, Alain eLife Computational and Systems Biology 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 B(act) 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. eLife Sciences Publications, Ltd 2022-06-13 /pmc/articles/PMC9236610/ /pubmed/35695373 http://dx.doi.org/10.7554/eLife.73888 Text en © 2022, Kumar et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Computational and Systems Biology
Kumar, Jayashree
Lackey, Lela
Waldern, Justin M
Dey, Abhishek
Mustoe, Anthony M
Weeks, Kevin M
Mathews, David H
Laederach, Alain
Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA 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 Computational and Systems Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9236610/
https://www.ncbi.nlm.nih.gov/pubmed/35695373
http://dx.doi.org/10.7554/eLife.73888
work_keys_str_mv AT kumarjayashree quantitativepredictionofvarianteffectsonalternativesplicinginmaptusingendogenouspremessengerrnastructureprobing
AT lackeylela quantitativepredictionofvarianteffectsonalternativesplicinginmaptusingendogenouspremessengerrnastructureprobing
AT waldernjustinm quantitativepredictionofvarianteffectsonalternativesplicinginmaptusingendogenouspremessengerrnastructureprobing
AT deyabhishek quantitativepredictionofvarianteffectsonalternativesplicinginmaptusingendogenouspremessengerrnastructureprobing
AT mustoeanthonym quantitativepredictionofvarianteffectsonalternativesplicinginmaptusingendogenouspremessengerrnastructureprobing
AT weekskevinm quantitativepredictionofvarianteffectsonalternativesplicinginmaptusingendogenouspremessengerrnastructureprobing
AT mathewsdavidh quantitativepredictionofvarianteffectsonalternativesplicinginmaptusingendogenouspremessengerrnastructureprobing
AT laederachalain quantitativepredictionofvarianteffectsonalternativesplicinginmaptusingendogenouspremessengerrnastructureprobing