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Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation

Chromatin accessibility mapping is a powerful approach to identify potential regulatory elements. A popular example is ATAC-seq, whereby Tn5 transposase inserts sequencing adapters into accessible DNA (‘tagmentation’). CUT&Tag is a tagmentation-based epigenomic profiling method in which antibody...

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Autores principales: Henikoff, Steven, Henikoff, Jorja G, Kaya-Okur, Hatice S, Ahmad, Kami
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7721439/
https://www.ncbi.nlm.nih.gov/pubmed/33191916
http://dx.doi.org/10.7554/eLife.63274
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author Henikoff, Steven
Henikoff, Jorja G
Kaya-Okur, Hatice S
Ahmad, Kami
author_facet Henikoff, Steven
Henikoff, Jorja G
Kaya-Okur, Hatice S
Ahmad, Kami
author_sort Henikoff, Steven
collection PubMed
description Chromatin accessibility mapping is a powerful approach to identify potential regulatory elements. A popular example is ATAC-seq, whereby Tn5 transposase inserts sequencing adapters into accessible DNA (‘tagmentation’). CUT&Tag is a tagmentation-based epigenomic profiling method in which antibody tethering of Tn5 to a chromatin epitope of interest profiles specific chromatin features in small samples and single cells. Here, we show that by simply modifying the tagmentation conditions for histone H3K4me2 or H3K4me3 CUT&Tag, antibody-tethered tagmentation of accessible DNA sites is redirected to produce chromatin accessibility maps that are indistinguishable from the best ATAC-seq maps. Thus, chromatin accessibility maps can be produced in parallel with CUT&Tag maps of other epitopes with all steps from nuclei to amplified sequencing-ready libraries performed in single PCR tubes in the laboratory or on a home workbench. As H3K4 methylation is produced by transcription at promoters and enhancers, our method identifies transcription-coupled accessible regulatory sites.
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spelling pubmed-77214392020-12-09 Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation Henikoff, Steven Henikoff, Jorja G Kaya-Okur, Hatice S Ahmad, Kami eLife Chromosomes and Gene Expression Chromatin accessibility mapping is a powerful approach to identify potential regulatory elements. A popular example is ATAC-seq, whereby Tn5 transposase inserts sequencing adapters into accessible DNA (‘tagmentation’). CUT&Tag is a tagmentation-based epigenomic profiling method in which antibody tethering of Tn5 to a chromatin epitope of interest profiles specific chromatin features in small samples and single cells. Here, we show that by simply modifying the tagmentation conditions for histone H3K4me2 or H3K4me3 CUT&Tag, antibody-tethered tagmentation of accessible DNA sites is redirected to produce chromatin accessibility maps that are indistinguishable from the best ATAC-seq maps. Thus, chromatin accessibility maps can be produced in parallel with CUT&Tag maps of other epitopes with all steps from nuclei to amplified sequencing-ready libraries performed in single PCR tubes in the laboratory or on a home workbench. As H3K4 methylation is produced by transcription at promoters and enhancers, our method identifies transcription-coupled accessible regulatory sites. eLife Sciences Publications, Ltd 2020-11-16 /pmc/articles/PMC7721439/ /pubmed/33191916 http://dx.doi.org/10.7554/eLife.63274 Text en © 2020, Henikoff et al http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Chromosomes and Gene Expression
Henikoff, Steven
Henikoff, Jorja G
Kaya-Okur, Hatice S
Ahmad, Kami
Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation
title Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation
title_full Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation
title_fullStr Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation
title_full_unstemmed Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation
title_short Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation
title_sort efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation
topic Chromosomes and Gene Expression
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7721439/
https://www.ncbi.nlm.nih.gov/pubmed/33191916
http://dx.doi.org/10.7554/eLife.63274
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