Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation

Seungbyn Baek, Insuk Lee

Research output: Contribution to journalReview articlepeer-review

4 Citations (Scopus)

Abstract

Most genetic variations associated with human complex traits are located in non-coding genomic regions. Therefore, understanding the genotype-to-phenotype axis requires a comprehensive catalog of functional non-coding genomic elements, most of which are involved in epigenetic regulation of gene expression. Genome-wide maps of open chromatin regions can facilitate functional analysis of cis- and trans-regulatory elements via their connections with trait-associated sequence variants. Currently, Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) is considered the most accessible and cost-effective strategy for genome-wide profiling of chromatin accessibility. Single-cell ATAC-seq (scATAC-seq) technology has also been developed to study cell type-specific chromatin accessibility in tissue samples containing a heterogeneous cellular population. However, due to the intrinsic nature of scATAC-seq data, which are highly noisy and sparse, accurate extraction of biological signals and devising effective biological hypothesis are difficult. To overcome such limitations in scATAC-seq data analysis, new methods and software tools have been developed over the past few years. Nevertheless, there is no consensus for the best practice of scATAC-seq data analysis yet. In this review, we discuss scATAC-seq technology and data analysis methods, ranging from preprocessing to downstream analysis, along with an up-to-date list of published studies that involved the application of this method. We expect this review will provide a guideline for successful data generation and analysis methods using appropriate software tools and databases for the study of chromatin accessibility at single-cell resolution.

Original languageEnglish
Pages (from-to)1429-1439
Number of pages11
JournalComputational and Structural Biotechnology Journal
Volume18
DOIs
Publication statusPublished - 2020

Bibliographical note

Funding Information:
This study was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) ( 2018M3C9A5064709 , 2018R1A5A2025079 , 2019M3A9B6065192 ) and Brain Korea 21 (BK21) PLUS program .

Publisher Copyright:
© 2020 The Author(s)

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Biophysics
  • Structural Biology
  • Biochemistry
  • Genetics
  • Computer Science Applications

Fingerprint Dive into the research topics of 'Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation'. Together they form a unique fingerprint.

Cite this