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Screening for functional regulatory variants in open chromatin using GenIE-ATAC
Understanding the effects of genetic variation in gene regulatory elements is crucial to interpreting genome function. This is particularly pertinent for the hundreds of thousands of disease-associated variants identified by GWAS, which frequently sit within gene regulatory elements but whose functi...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10287956/ https://www.ncbi.nlm.nih.gov/pubmed/37125635 http://dx.doi.org/10.1093/nar/gkad332 |
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author | Cooper, Sarah Schwartzentruber, Jeremy Coomber, Eve L Wu, Qianxin Bassett, Andrew |
author_facet | Cooper, Sarah Schwartzentruber, Jeremy Coomber, Eve L Wu, Qianxin Bassett, Andrew |
author_sort | Cooper, Sarah |
collection | PubMed |
description | Understanding the effects of genetic variation in gene regulatory elements is crucial to interpreting genome function. This is particularly pertinent for the hundreds of thousands of disease-associated variants identified by GWAS, which frequently sit within gene regulatory elements but whose functional effects are often unknown. Current methods are limited in their scalability and ability to assay regulatory variants in their endogenous context, independently of other tightly linked variants. Here, we present a new medium-throughput screening system: genome engineering based interrogation of enhancers assay for transposase accessible chromatin (GenIE-ATAC), that measures the effect of individual variants on chromatin accessibility in their endogenous genomic and chromatin context. We employ this assay to screen for the effects of regulatory variants in human induced pluripotent stem cells, validating a subset of causal variants, and extend our software package (rgenie) to analyse these new data. We demonstrate that this methodology can be used to understand the impact of defined deletions and point mutations within transcription factor binding sites. We thus establish GenIE-ATAC as a method to screen for the effect of gene regulatory element variation, allowing identification and prioritisation of causal variants from GWAS for functional follow-up and understanding the mechanisms of regulatory element function. |
format | Online Article Text |
id | pubmed-10287956 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-102879562023-06-24 Screening for functional regulatory variants in open chromatin using GenIE-ATAC Cooper, Sarah Schwartzentruber, Jeremy Coomber, Eve L Wu, Qianxin Bassett, Andrew Nucleic Acids Res Methods Online Understanding the effects of genetic variation in gene regulatory elements is crucial to interpreting genome function. This is particularly pertinent for the hundreds of thousands of disease-associated variants identified by GWAS, which frequently sit within gene regulatory elements but whose functional effects are often unknown. Current methods are limited in their scalability and ability to assay regulatory variants in their endogenous context, independently of other tightly linked variants. Here, we present a new medium-throughput screening system: genome engineering based interrogation of enhancers assay for transposase accessible chromatin (GenIE-ATAC), that measures the effect of individual variants on chromatin accessibility in their endogenous genomic and chromatin context. We employ this assay to screen for the effects of regulatory variants in human induced pluripotent stem cells, validating a subset of causal variants, and extend our software package (rgenie) to analyse these new data. We demonstrate that this methodology can be used to understand the impact of defined deletions and point mutations within transcription factor binding sites. We thus establish GenIE-ATAC as a method to screen for the effect of gene regulatory element variation, allowing identification and prioritisation of causal variants from GWAS for functional follow-up and understanding the mechanisms of regulatory element function. Oxford University Press 2023-05-01 /pmc/articles/PMC10287956/ /pubmed/37125635 http://dx.doi.org/10.1093/nar/gkad332 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methods Online Cooper, Sarah Schwartzentruber, Jeremy Coomber, Eve L Wu, Qianxin Bassett, Andrew Screening for functional regulatory variants in open chromatin using GenIE-ATAC |
title | Screening for functional regulatory variants in open chromatin using GenIE-ATAC |
title_full | Screening for functional regulatory variants in open chromatin using GenIE-ATAC |
title_fullStr | Screening for functional regulatory variants in open chromatin using GenIE-ATAC |
title_full_unstemmed | Screening for functional regulatory variants in open chromatin using GenIE-ATAC |
title_short | Screening for functional regulatory variants in open chromatin using GenIE-ATAC |
title_sort | screening for functional regulatory variants in open chromatin using genie-atac |
topic | Methods Online |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10287956/ https://www.ncbi.nlm.nih.gov/pubmed/37125635 http://dx.doi.org/10.1093/nar/gkad332 |
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