Cargando…
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...
Autores principales: | , , , |
---|---|
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 |
_version_ | 1783620020581957632 |
---|---|
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. |
format | Online Article Text |
id | pubmed-7721439 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | eLife Sciences Publications, Ltd |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT henikoffsteven efficientchromatinaccessibilitymappinginsitubynucleosometetheredtagmentation AT henikoffjorjag efficientchromatinaccessibilitymappinginsitubynucleosometetheredtagmentation AT kayaokurhatices efficientchromatinaccessibilitymappinginsitubynucleosometetheredtagmentation AT ahmadkami efficientchromatinaccessibilitymappinginsitubynucleosometetheredtagmentation |