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ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation
BACKGROUND: Chromatin dysregulation is associated with developmental disorders and cancer. Numerous methods for measuring genome-wide chromatin accessibility have been developed in the genomic era to interrogate the function of chromatin regulators. A recent technique which has gained widespread use...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7178746/ https://www.ncbi.nlm.nih.gov/pubmed/32321567 http://dx.doi.org/10.1186/s13072-020-00342-y |
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author | Reske, Jake J. Wilson, Mike R. Chandler, Ronald L. |
author_facet | Reske, Jake J. Wilson, Mike R. Chandler, Ronald L. |
author_sort | Reske, Jake J. |
collection | PubMed |
description | BACKGROUND: Chromatin dysregulation is associated with developmental disorders and cancer. Numerous methods for measuring genome-wide chromatin accessibility have been developed in the genomic era to interrogate the function of chromatin regulators. A recent technique which has gained widespread use due to speed and low input requirements with native chromatin is the Assay for Transposase-Accessible Chromatin, or ATAC-seq. Biologists have since used this method to compare chromatin accessibility between two cellular conditions. However, approaches for calculating differential accessibility can yield conflicting results, and little emphasis is placed on choice of normalization method during differential ATAC-seq analysis, especially when global chromatin alterations might be expected. RESULTS: Using an in vivo ATAC-seq data set generated in our recent report, we observed differences in chromatin accessibility patterns depending on the data normalization method used to calculate differential accessibility. This observation was further verified on published ATAC-seq data from yeast. We propose a generalized workflow for differential accessibility analysis using ATAC-seq data. We further show this workflow identifies sites of differential chromatin accessibility that correlate with gene expression and is sensitive to differential analysis using negative controls. CONCLUSIONS: We argue that researchers should systematically compare multiple normalization methods before continuing with differential accessibility analysis. ATAC-seq users should be aware of the interpretations of potential bias within experimental data and the assumptions of the normalization method implemented. |
format | Online Article Text |
id | pubmed-7178746 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-71787462020-04-26 ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation Reske, Jake J. Wilson, Mike R. Chandler, Ronald L. Epigenetics Chromatin Methodology BACKGROUND: Chromatin dysregulation is associated with developmental disorders and cancer. Numerous methods for measuring genome-wide chromatin accessibility have been developed in the genomic era to interrogate the function of chromatin regulators. A recent technique which has gained widespread use due to speed and low input requirements with native chromatin is the Assay for Transposase-Accessible Chromatin, or ATAC-seq. Biologists have since used this method to compare chromatin accessibility between two cellular conditions. However, approaches for calculating differential accessibility can yield conflicting results, and little emphasis is placed on choice of normalization method during differential ATAC-seq analysis, especially when global chromatin alterations might be expected. RESULTS: Using an in vivo ATAC-seq data set generated in our recent report, we observed differences in chromatin accessibility patterns depending on the data normalization method used to calculate differential accessibility. This observation was further verified on published ATAC-seq data from yeast. We propose a generalized workflow for differential accessibility analysis using ATAC-seq data. We further show this workflow identifies sites of differential chromatin accessibility that correlate with gene expression and is sensitive to differential analysis using negative controls. CONCLUSIONS: We argue that researchers should systematically compare multiple normalization methods before continuing with differential accessibility analysis. ATAC-seq users should be aware of the interpretations of potential bias within experimental data and the assumptions of the normalization method implemented. BioMed Central 2020-04-22 /pmc/articles/PMC7178746/ /pubmed/32321567 http://dx.doi.org/10.1186/s13072-020-00342-y Text en © The Author(s) 2020 Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Methodology Reske, Jake J. Wilson, Mike R. Chandler, Ronald L. ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation |
title | ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation |
title_full | ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation |
title_fullStr | ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation |
title_full_unstemmed | ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation |
title_short | ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation |
title_sort | atac-seq normalization method can significantly affect differential accessibility analysis and interpretation |
topic | Methodology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7178746/ https://www.ncbi.nlm.nih.gov/pubmed/32321567 http://dx.doi.org/10.1186/s13072-020-00342-y |
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