Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data  

作　　者：Siyuan Cheng Benpeng Miao Tiandao Li Guoyan Zhao Bo Zhang 

机构地区：[1]Department of Developmental Biology,Center of Regenerative Medicine,Washington University School of Medicine,St.Louis,MO 63108,USA [2]Department of Genetics,Washington University School of Medicine,St.Louis,MO 63108,USA [3]Department of Neurology,Washington University School of Medicine,St.Louis,MO 63108,USA [4]Department of Pathology and Immunology,Washington University School of Medicine,St.Louis,MO 63108,USA

出　　处：《Genomics, Proteomics & Bioinformatics》2024年第3期11-27,共17页基因组蛋白质组与生物信息学报（英文版）

基　　金：supported by the National Institutes of Health,USA(Grant Nos.R35GM142917 to Bo Zhang,U24ES026699 to Bo Zhang,R25DA027995 to Bo Zhang,R03AG070474 to Guoyan Zhao,R01NS123571 to Guoyan Zhao,U19NS130607 to Guoyan Zhao,and U24HG012070 to Bo Zhang and Guoyan Zhao);National Institutes of Health,USA.

摘　　要：Efficient and reliable profiling methods are essential to study epigenetics.Tn5,one of the first identified prokaryotic transposases with high DNA-binding and tagmentation efficiency,is widely adopted in different genomic and epigenomic protocols for high-throughputly exploring the genome and epigenome.Based on Tn5,the Assay for Transposase-Accessible Chromatin using sequencing(ATAC-seq)and the Cleavage Under Targets and Tagmentation(CUT&Tag)were developed to measure chromatin accessibility and detect DNA–protein interactions.These methodologies can be applied to large amounts of biological samples with low-input levels,such as rare tissues,embryos,and sorted single cells.However,fast and proper processing of these epigenomic data has become a bottleneck because massive data production continues to increase quickly.Furthermore,inappropriate data analysis can generate biased or misleading conclusions.Therefore,it is essential to evaluate the performance of Tn5-based ATAC-seq and CUT&Tag data processing bioinformatics tools,many of which were developed mostly for analyzing chromatin immunoprecipitation followed by sequencing(ChIP-seq)data.Here,we conducted a comprehensive benchmarking analysis to evaluate the performance of eight popular software for processing ATAC-seq and CUT&Tag data.We compared the sensitivity,specificity,and peak width distribution for both narrow-type and broad-type peak calling.We also tested the influence of the availability of control IgG input in CUT&Tag data analysis.Finally,we evaluated the differential analysis strategies commonly used for analyzing the CUT&Tag data.Our study provided comprehensive guidance for selecting bioinformatics tools and recommended analysis strategies,which were implemented into Docker/Singularity images for streamlined data analysis.

关 键 词：Tn5 transposase EPIGENETIC BIOINFORMATICS ATAC-seq CUT&Tag 

分 类 号：Q811.4[生物学—生物工程]