The Chromatin Accessibility Landscape of Nonalcoholic Fatty Liver Disease Progression

Byeonggeun Kang, Byunghee Kang, Tae Young Roh, Rho Hyun Seong, Won Kim

Research output: Contribution to journalArticlepeer-review

10 Scopus citations

Abstract

The advent of the assay for transposase-accessible chromatin using sequencing (ATAC-seq) has shown great potential as a leading method for analyzing the genome-wide profiling of chromatin accessibility. A comprehensive reference to the ATAC-seq dataset for disease progression is important for understanding the regulatory specificity caused by genetic or epigenetic changes. In this study, we present a genome-wide chromatin accessibility profile of 44 liver samples spanning the full histological spectrum of nonalcoholic fatty liver disease (NAFLD). We analyzed the ATAC-seq signal enrichment, fragment size distribution, and correlation coefficients according to the histological severity of NAFLD (healthy control vs steatosis vs fibrotic nonalcoholic steatohepatitis), demonstrating the high quality of the dataset. Consequently, 112,303 merged regions (genomic regions containing one or multiple overlapping peak regions) were identified. Additionally, we found differentially accessible regions (DARs) and performed transcription factor binding motif enrichment analysis and de novo motif analysis to determine new biomarker candidates. These data revealed the gene-regulatory interactions and noncoding factors that can affect NAFLD progression. In summary, our study provides a valuable resource for the human epigenome by applying an advanced approach to facilitate diagnosis and treatment by understanding the non-coding genome of NAFLD.

Original languageEnglish
Pages (from-to)343-352
Number of pages10
JournalMolecules and Cells
Volume45
Issue number5
DOIs
StatePublished - 31 May 2022

Bibliographical note

Publisher Copyright:
© 2022, Korean Society for Molecular and Cellular Biology. All rights reserved.

Keywords

  • assay for transposase-accessible chromatin using

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