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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Diabetes Association
2020
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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. |
format | Online Article Text |
id | pubmed-7679775 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | American Diabetes Association |
record_format | MEDLINE/PubMed |
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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