GoPeaks: histone modification peak calling for CUT&Tag

Genome-wide mapping of histone modifications is critical to understanding transcriptional regulation. CUT&Tag is a new method for profiling histone modifications, offering improved sensitivity and decreased cost compared with ChIP-seq. Here, we present GoPeaks, a peak calling method specifically...

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Autores principales: Yashar, William M., Kong, Garth, VanCampen, Jake, Curtiss, Brittany M., Coleman, Daniel J., Carbone, Lucia, Yardimci, Galip Gürkan, Maxson, Julia E., Braun, Theodore P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252088/
https://www.ncbi.nlm.nih.gov/pubmed/35788238
http://dx.doi.org/10.1186/s13059-022-02707-w
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author Yashar, William M.
Kong, Garth
VanCampen, Jake
Curtiss, Brittany M.
Coleman, Daniel J.
Carbone, Lucia
Yardimci, Galip Gürkan
Maxson, Julia E.
Braun, Theodore P.
author_facet Yashar, William M.
Kong, Garth
VanCampen, Jake
Curtiss, Brittany M.
Coleman, Daniel J.
Carbone, Lucia
Yardimci, Galip Gürkan
Maxson, Julia E.
Braun, Theodore P.
author_sort Yashar, William M.
collection PubMed
description Genome-wide mapping of histone modifications is critical to understanding transcriptional regulation. CUT&Tag is a new method for profiling histone modifications, offering improved sensitivity and decreased cost compared with ChIP-seq. Here, we present GoPeaks, a peak calling method specifically designed for histone modification CUT&Tag data. We compare the performance of GoPeaks against commonly used peak calling algorithms to detect histone modifications that display a range of peak profiles and are frequently used in epigenetic studies. We find that GoPeaks robustly detects genome-wide histone modifications and, notably, identifies a substantial number of H3K27ac peaks with improved sensitivity compared to other standard algorithms. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02707-w.
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spelling pubmed-92520882022-07-05 GoPeaks: histone modification peak calling for CUT&Tag Yashar, William M. Kong, Garth VanCampen, Jake Curtiss, Brittany M. Coleman, Daniel J. Carbone, Lucia Yardimci, Galip Gürkan Maxson, Julia E. Braun, Theodore P. Genome Biol Method Genome-wide mapping of histone modifications is critical to understanding transcriptional regulation. CUT&Tag is a new method for profiling histone modifications, offering improved sensitivity and decreased cost compared with ChIP-seq. Here, we present GoPeaks, a peak calling method specifically designed for histone modification CUT&Tag data. We compare the performance of GoPeaks against commonly used peak calling algorithms to detect histone modifications that display a range of peak profiles and are frequently used in epigenetic studies. We find that GoPeaks robustly detects genome-wide histone modifications and, notably, identifies a substantial number of H3K27ac peaks with improved sensitivity compared to other standard algorithms. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02707-w. BioMed Central 2022-07-04 /pmc/articles/PMC9252088/ /pubmed/35788238 http://dx.doi.org/10.1186/s13059-022-02707-w Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/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/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://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 Method
Yashar, William M.
Kong, Garth
VanCampen, Jake
Curtiss, Brittany M.
Coleman, Daniel J.
Carbone, Lucia
Yardimci, Galip Gürkan
Maxson, Julia E.
Braun, Theodore P.
GoPeaks: histone modification peak calling for CUT&Tag
title GoPeaks: histone modification peak calling for CUT&Tag
title_full GoPeaks: histone modification peak calling for CUT&Tag
title_fullStr GoPeaks: histone modification peak calling for CUT&Tag
title_full_unstemmed GoPeaks: histone modification peak calling for CUT&Tag
title_short GoPeaks: histone modification peak calling for CUT&Tag
title_sort gopeaks: histone modification peak calling for cut&tag
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252088/
https://www.ncbi.nlm.nih.gov/pubmed/35788238
http://dx.doi.org/10.1186/s13059-022-02707-w
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