Regulatory domains controlling high intestinal vitamin D receptor gene expression are conserved in mouse and human

James C Fleet,Dennis Aldea,Lei Chen,Sylvia Christakos,Michael Verzi

doi:10.1016/j.jbc.2022.101616

Abstract

Vitamin D receptor (VDR) levels are highest in the intestine where it mediates 1,25 dihydroxyvitamin D-induced gene expression. However, the mechanisms controlling high intestinal VDR gene expression are unknown. Here, we used Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-Seq) to identify the regulatory sites controlling intestine-specific Vdr gene expression in the small intestine (villi and crypts) and colon of developing, adult, and aged mice. We identified 17 ATAC peaks in a 125 kb region from intron 3 to −55.8 kb from exon 1 of the Vdr gene. Interestingly, many of these peaks were missing/reduced in the developing intestine. Chromatin ImmunoPrecipitation-Sequencing (ChIP-Seq) peaks for intestinal transcription factors (TFs) were present within the ATAC peaks and at HiChIP looping attachments that connected the ATAC/TF ChIP peaks to the transcription start site and CCCTF-binding factor sites at the borders of the Vdr gene regulatory domain. Intestine-specific regulatory sites were identified by comparing ATAC peaks to DNAse-Seq data from other tissues that revealed tissue-specific, evolutionary conserved, and species-specific peaks. Bioinformatics analysis of human DNAse-Seq peaks revealed polymorphisms that disrupt TF-binding sites. Our analysis shows that mouse intestinal Vdr gene regulation requires a complex interaction of multiple distal regulatory regions and is controlled by a combination of intestinal TFs. These intestinal regulatory sites are well conserved in humans suggesting that they may be key components of VDR regulation in both mouse and human intestines.

Highlights

Vitamin D is a nutrient that serves as the precursor for 1,25 dihydroxyvitamin D (1,25(OH)2D), a hormone that controls a wide variety of biological processes relevant to human health [1]
To define the regulatory region within the mouse Vdr gene topologically associated domains (TAD), we examined how the ATAC peaks we generated from the small intestine villi related to Hi-C data from CH12 cells [20]
Our data clearly show that the high-level expression of vitamin D receptor (VDR) in the intestine is controlled by a regulatory network of transcription factors acting at multiple upstream and downstream DNA sequences

Summary

Introduction

Vitamin D is a nutrient that serves as the precursor for 1,25 dihydroxyvitamin D (1,25(OH)2D), a hormone that controls a wide variety of biological processes relevant to human health [1]. We report the results from primary ATAC-seq and Hi-ChIP data to identify the active regulatory domain of the mouse Vdr gene We integrated this data with publicly available ChIP-seq data combined with transcription factor binding site analysis of these regulatory regions to define the critical transcription factors controlling mouse intestinal Vdr gene expression. We compared our data to DNAse-seq or ATAC-seq data from other mouse tissues and from human small intestine to identify the tissue-specific and evolutionarily conserved regulatory regions controlling human intestinal VDR gene expression. These results provide a clear picture of the regulatory complexity controlling Vdr gene expression in the intestine

Results

Discussion

Experimental Procedures