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Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding
Functional variants in the genome are usually identified by their association with local gene expression, DNA methylation or chromatin states. DNA sequence motif analysis and chromatin immunoprecipitation studies have provided indirect support for the hypothesis that functional variants alter transc...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6677801/ https://www.ncbi.nlm.nih.gov/pubmed/31375681 http://dx.doi.org/10.1038/s41467-019-11412-5 |
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author | Johnston, Andrew D. Simões-Pires, Claudia A. Thompson, Taylor V. Suzuki, Masako Greally, John M. |
author_facet | Johnston, Andrew D. Simões-Pires, Claudia A. Thompson, Taylor V. Suzuki, Masako Greally, John M. |
author_sort | Johnston, Andrew D. |
collection | PubMed |
description | Functional variants in the genome are usually identified by their association with local gene expression, DNA methylation or chromatin states. DNA sequence motif analysis and chromatin immunoprecipitation studies have provided indirect support for the hypothesis that functional variants alter transcription factor binding to exert their effects. In this study, we provide direct evidence that functional variants can alter transcription factor binding. We identify a multifunctional variant within the TBC1D4 gene encoding a canonical NFκB binding site, and edited it using CRISPR-Cas9 to remove this site. We show that this editing reduces TBC1D4 expression, local chromatin accessibility and binding of the p65 component of NFκB. We then used CRISPR without genomic editing to guide p65 back to the edited locus, demonstrating that this re-targeting, occurring ~182 kb from the gene promoter, is enough to restore the function of the locus, supporting the central role of transcription factors mediating the effects of functional variants. |
format | Online Article Text |
id | pubmed-6677801 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-66778012019-08-05 Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding Johnston, Andrew D. Simões-Pires, Claudia A. Thompson, Taylor V. Suzuki, Masako Greally, John M. Nat Commun Article Functional variants in the genome are usually identified by their association with local gene expression, DNA methylation or chromatin states. DNA sequence motif analysis and chromatin immunoprecipitation studies have provided indirect support for the hypothesis that functional variants alter transcription factor binding to exert their effects. In this study, we provide direct evidence that functional variants can alter transcription factor binding. We identify a multifunctional variant within the TBC1D4 gene encoding a canonical NFκB binding site, and edited it using CRISPR-Cas9 to remove this site. We show that this editing reduces TBC1D4 expression, local chromatin accessibility and binding of the p65 component of NFκB. We then used CRISPR without genomic editing to guide p65 back to the edited locus, demonstrating that this re-targeting, occurring ~182 kb from the gene promoter, is enough to restore the function of the locus, supporting the central role of transcription factors mediating the effects of functional variants. Nature Publishing Group UK 2019-08-02 /pmc/articles/PMC6677801/ /pubmed/31375681 http://dx.doi.org/10.1038/s41467-019-11412-5 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Johnston, Andrew D. Simões-Pires, Claudia A. Thompson, Taylor V. Suzuki, Masako Greally, John M. Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding |
title | Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding |
title_full | Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding |
title_fullStr | Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding |
title_full_unstemmed | Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding |
title_short | Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding |
title_sort | functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6677801/ https://www.ncbi.nlm.nih.gov/pubmed/31375681 http://dx.doi.org/10.1038/s41467-019-11412-5 |
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