Fundamental and practical approaches for single-cell ATAC-seq analysis

IF 4.6 4区 农林科学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Peiyu Shi, Yage Nie, Jiawen Yang, Weixing Zhang, Zhongjie Tang, Jin Xu
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引用次数: 1

Abstract

Assays for transposase-accessible chromatin through high-throughput sequencing (ATAC-seq) are effective tools in the study of genome-wide chromatin accessibility landscapes. With the rapid development of single-cell technology, open chromatin regions that play essential roles in epigenetic regulation have been measured at the single-cell level using single-cell ATAC-seq approaches. The application of scATAC-seq has become as popular as that of scRNA-seq. However, owing to the nature of scATAC-seq data, which are sparse and noisy, processing the data requires different methodologies and empirical experience. This review presents a practical guide for processing scATAC-seq data, from quality evaluation to downstream analysis, for various applications. In addition to the epigenomic profiling from scATAC-seq, we also discuss recent studies in which the function of non-coding variants has been investigated based on cell type-specific cis-regulatory elements and how to use the by-product genetic information obtained from scATAC-seq to infer single-cell copy number variants and trace cell lineage. We anticipate that this review will assist researchers in designing and implementing scATAC-seq assays to facilitate research in diverse fields.

单细胞ATAC-seq分析的基本和实用方法
通过高通量测序(ATAC-seq)检测转座酶可及染色质是研究全基因组染色质可及性景观的有效工具。随着单细胞技术的快速发展,已经使用单细胞ATAC-seq方法在单细胞水平上测量了在表观遗传学调控中发挥重要作用的开放染色质区域。scATAC-seq的应用已经变得和scRNA-seq一样流行。然而,由于scATAC-seq数据的稀疏性和噪声性,处理数据需要不同的方法和经验。这篇综述为各种应用提供了处理scATAC-seq数据的实用指南,从质量评估到下游分析。除了来自scATAC-seq的表观基因组分析外,我们还讨论了最近的研究,其中基于细胞类型特异性顺式调控元件研究了非编码变体的功能,以及如何使用从scATAC-seq获得的副产物遗传信息来推断单细胞拷贝数变体和追踪细胞谱系。我们预计这篇综述将有助于研究人员设计和实施scATAC-seq分析,以促进不同领域的研究。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
CiteScore
7.70
自引率
2.80%
发文量
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