Abstract
Genome-wide mapping of the histone modification landscape is critical to understanding tran-scriptional regulation. Cleavage Under Targets and Tagmentation (CUT&Tag) is a new method for profiling the localization of covalent histone modifications, offering improved sensitivity and decreased cost compared with Chromatin Immunoprecipitation Sequencing (ChIP-seq). Here, we present GoPeaks, a peak calling method specifically designed for histone modification CUT&Tag data. GoPeaks implements a Binomial distribution and stringent read count cut-off to nominate candidate genomic regions. We compared the performance of GoPeaks against commonly used peak calling algorithms to detect H3K4me3, H3K4me1, and H3K27Ac peaks from CUT&Tag data. These histone modifications display a range of peak profiles and are frequently used in epigenetic studies. We found GoPeaks robustly detects genome-wide histone modifications and, notably, identifies H3K27Ac with improved sensitivity compared to other standard peak calling algorithms.
Competing Interest Statement
WMY potential competing interests -- WMY is a former employee of Abreos Biosciences, Inc. and was compensated in part with common stock options. Pursuant to the merger and reorganization agreement between Abreos Biosciences, Inc. and Fimafeng, Inc., WMY surrendered all of his common stock options in 03/2021. JEM -- SAB: Ionis pharmaceuticals, Research Funding: Gilead Sciences. The other authors do not have competing interests, financial or otherwise.
Footnotes
Removed the inappropriate hyphenations in the abstract, which were the result of Microsoft Word's auto-hyphenation feature. Updated competing interests statement. Adjusted figures for bioRxiv watermark.
