Combined analysis of dissimilar promoter accessibility and gene expression profiles identifies tissue-specific genes and actively repressed networks.

Epigenetics & Chromatin
Rebekah R StarksGeetu Tuteja

Abstract

The assay for transposase-accessible chromatin (ATAC-seq) is a powerful method to examine chromatin accessibility. While many studies have reported a positive correlation between gene expression and promoter accessibility, few have investigated the genes that deviate from this trend. In this study, we aimed to understand the relationship between gene expression and promoter accessibility in multiple cell types while also identifying gene regulatory networks in the placenta, an understudied organ that is critical for a successful pregnancy. We started by assaying the open chromatin landscape in the mid-gestation placenta, when the fetal vasculature has started developing. After incorporating transcriptomic data generated in the placenta at the same time point, we grouped genes based on their expression levels and ATAC-seq promoter coverage. We found that the genes with the strongest correlation (high expression and high coverage) are likely involved in housekeeping functions, whereas tissue-specific genes were highly expressed and had only medium-low coverage. We also predicted that genes with medium-low expression and high promoter coverage were actively repressed. Within this group, we extracted a protein-protein interaction n...Continue Reading

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Citations

Jun 6, 2020·Journal of the Endocrine Society·Adeline DivouxSteven R Smith
Dec 15, 2020·Immunology and Cell Biology·Raymond Hy Louie, Fabio Luciani
Nov 12, 2020·International Journal of Molecular Sciences·Rebekah R StarksGeetu Tuteja
May 4, 2021·Journal of Animal Science and Biotechnology·Jingwei YueLongchao Zhang
Jul 9, 2021·NAR Genomics and Bioinformatics·Thomas FauxLaura L Elo
Sep 17, 2021·Proceedings of the National Academy of Sciences of the United States of America·Hiroyoshi DoiKinichi Nakashima

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Methods Mentioned

BETA
gene knockout
immunoprecipitation
RNA-seq
ChIP-seq
ChIP

Software Mentioned

Genomic Regions Enrichment of Annotations Tool [ ( GREAT )
Trimmomatic
nuScore
GREAT
FastQC
HISAT2
PRISM
UCSC genome browser
Genomic Regions Enrichment of Annotation Tool ( GREAT )
Cytoscape

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