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In Vivo Reporter Assays Uncover Changes in Enhancer Activity Caused by Type 2 Diabetes–Associated Single Nucleotide Polymorphisms

Many single nucleotide polymorphisms (SNPs) associated with type 2 diabetes overlap with putative endocrine pancreatic enhancers, suggesting that these SNPs modulate enhancer activity and, consequently, gene expression. We performed in vivo mosaic transgenesis assays in zebrafish to quantitatively t...

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Autores principales: Eufrásio, Ana, Perrod, Chiara, Ferreira, Fábio J., Duque, Marta, Galhardo, Mafalda, Bessa, José
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Diabetes Association 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7679775/
https://www.ncbi.nlm.nih.gov/pubmed/32912862
http://dx.doi.org/10.2337/db19-1049
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author Eufrásio, Ana
Perrod, Chiara
Ferreira, Fábio J.
Duque, Marta
Galhardo, Mafalda
Bessa, José
author_facet Eufrásio, Ana
Perrod, Chiara
Ferreira, Fábio J.
Duque, Marta
Galhardo, Mafalda
Bessa, José
author_sort Eufrásio, Ana
collection PubMed
description Many single nucleotide polymorphisms (SNPs) associated with type 2 diabetes overlap with putative endocrine pancreatic enhancers, suggesting that these SNPs modulate enhancer activity and, consequently, gene expression. We performed in vivo mosaic transgenesis assays in zebrafish to quantitatively test the enhancer activity of type 2 diabetes–associated loci. Six out of 10 tested sequences are endocrine pancreatic enhancers. The risk variant of two sequences decreased enhancer activity, while in another two incremented it. One of the latter (rs13266634) locates in an SLC30A8 exon, encoding a tryptophan-to-arginine substitution that decreases SLC30A8 function, which is the canonical explanation for type 2 diabetes risk association. However, other type 2 diabetes–associated SNPs that truncate SLC30A8 confer protection from this disease, contradicting this explanation. Here, we clarify this incongruence, showing that rs13266634 boosts the activity of an overlapping enhancer and suggesting an SLC30A8 gain of function as the cause for the increased risk for the disease. We further dissected the functionality of this enhancer, finding a single nucleotide mutation sufficient to impair its activity. Overall, this work assesses in vivo the importance of disease-associated SNPs in the activity of endocrine pancreatic enhancers, including a poorly explored case where a coding SNP modulates the activity of an enhancer.
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spelling pubmed-76797752020-12-03 In Vivo Reporter Assays Uncover Changes in Enhancer Activity Caused by Type 2 Diabetes–Associated Single Nucleotide Polymorphisms Eufrásio, Ana Perrod, Chiara Ferreira, Fábio J. Duque, Marta Galhardo, Mafalda Bessa, José Diabetes Genetics/Genomes/Proteomics/Metabolomics Many single nucleotide polymorphisms (SNPs) associated with type 2 diabetes overlap with putative endocrine pancreatic enhancers, suggesting that these SNPs modulate enhancer activity and, consequently, gene expression. We performed in vivo mosaic transgenesis assays in zebrafish to quantitatively test the enhancer activity of type 2 diabetes–associated loci. Six out of 10 tested sequences are endocrine pancreatic enhancers. The risk variant of two sequences decreased enhancer activity, while in another two incremented it. One of the latter (rs13266634) locates in an SLC30A8 exon, encoding a tryptophan-to-arginine substitution that decreases SLC30A8 function, which is the canonical explanation for type 2 diabetes risk association. However, other type 2 diabetes–associated SNPs that truncate SLC30A8 confer protection from this disease, contradicting this explanation. Here, we clarify this incongruence, showing that rs13266634 boosts the activity of an overlapping enhancer and suggesting an SLC30A8 gain of function as the cause for the increased risk for the disease. We further dissected the functionality of this enhancer, finding a single nucleotide mutation sufficient to impair its activity. Overall, this work assesses in vivo the importance of disease-associated SNPs in the activity of endocrine pancreatic enhancers, including a poorly explored case where a coding SNP modulates the activity of an enhancer. American Diabetes Association 2020-12 2020-09-10 /pmc/articles/PMC7679775/ /pubmed/32912862 http://dx.doi.org/10.2337/db19-1049 Text en © 2020 by the American Diabetes Association https://www.diabetesjournals.org/content/licenseReaders may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered. More information is available at https://www.diabetesjournals.org/content/license.
spellingShingle Genetics/Genomes/Proteomics/Metabolomics
Eufrásio, Ana
Perrod, Chiara
Ferreira, Fábio J.
Duque, Marta
Galhardo, Mafalda
Bessa, José
In Vivo Reporter Assays Uncover Changes in Enhancer Activity Caused by Type 2 Diabetes–Associated Single Nucleotide Polymorphisms
title In Vivo Reporter Assays Uncover Changes in Enhancer Activity Caused by Type 2 Diabetes–Associated Single Nucleotide Polymorphisms
title_full In Vivo Reporter Assays Uncover Changes in Enhancer Activity Caused by Type 2 Diabetes–Associated Single Nucleotide Polymorphisms
title_fullStr In Vivo Reporter Assays Uncover Changes in Enhancer Activity Caused by Type 2 Diabetes–Associated Single Nucleotide Polymorphisms
title_full_unstemmed In Vivo Reporter Assays Uncover Changes in Enhancer Activity Caused by Type 2 Diabetes–Associated Single Nucleotide Polymorphisms
title_short In Vivo Reporter Assays Uncover Changes in Enhancer Activity Caused by Type 2 Diabetes–Associated Single Nucleotide Polymorphisms
title_sort in vivo reporter assays uncover changes in enhancer activity caused by type 2 diabetes–associated single nucleotide polymorphisms
topic Genetics/Genomes/Proteomics/Metabolomics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7679775/
https://www.ncbi.nlm.nih.gov/pubmed/32912862
http://dx.doi.org/10.2337/db19-1049
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