Regulatory interaction between the ZPBP2-ORMDL3/Zpbp2-Ormdl3 region and the circadian clock

Abstract

Genome-wide association study (GWAS) loci for several immunity-mediated diseases (early onset asthma, inflammatory bowel disease (IBD), primary biliary cholangitis, and rheumatoid arthritis) map to chromosomal region 17q12-q21. The predominant view is that association between 17q12-q21 alleles and increased risk of developing asthma or IBD is due to regulatory variants. ORM sphingolipid biosynthesis regulator (ORMDL3) residing in this region is the most promising gene candidate for explaining association with disease. However, the relationship between 17q12-q21 alleles and disease is complex suggesting contributions from other factors, such as trans-acting genetic and environmental modifiers or circadian rhythms. Circadian rhythms regulate expression levels of thousands of genes and their dysregulation is implicated in the etiology of several common chronic inflammatory diseases. However, their role in the regulation of the 17q12-q21 genes has not been investigated. Moreover, the core clock gene nuclear receptor subfamily 1, group D, member 1 (NR1D1) resides about 200 kb distal to the GWAS region. We hypothesized that circadian rhythms influenced gene expression levels in 17q12-q21 region and conversely, regulatory elements in this region influenced transcription of the core clock gene NR1D1 in cis. To test these hypotheses, we examined the diurnal expression profiles of zona pellucida binding protein 2 (ZPBP2/Zpbp2), gasdermin B (GSDMB), and ORMDL3/Ormdl3 in human and mouse tissues and analyzed the impact of genetic variation in the ZPBP2/Zpbp2 region on NR1D1/Nr1d1 expression. We found that Ormdl3 and Zpbp2 were controlled by the circadian clock in a tissue-specific fashion. We also report that deletion of the Zpbp2 region altered the expression profile of Nr1d1 in lungs and ileum in a time-dependent manner. In liver, the deletion was associated with enhanced expression of Ormdl3. We provide the first evidence that disease-associated genes Zpbp2 and Ormdl3 are regulated by circadian rhythms and the Zpbp2 region influences expression of the core clock gene Nr1d1.

Glucocorticoid receptor-mediated Nr1d1 chromatin circadian misalignment in stress-induced irritable bowel syndrome

“…In this region, we found that the WAS-induced Zpbp2-Ormdl3 chromatin loop replaced the Ikzf3-Ormdl3 and Ormdl3-Nr1d1 super-enhancer loops in control at the chromatin looping sites that include the GR bound Ikzf3 - Zpbp2 bidirectional promoter and Nr1d1 super-enhancer. 22 , 35 In addition, WAS elevated Nr1d1 super-enhancer GR binding ( Figure 4 B). This pattern correlates with IBS and IBD SNP rs2872507 regulates transcription of this region and IBD SNP (rs12936231) mediated long-range regulation of NR1D1 via the formation of IBD-related ZPBP2-ORMDL3 loop ( Figures 4 C and 4D).…”

“…In addition to IBS and IBD-related DEGs encoded within the conserved Nr1d1-Ormdl3-Ikzf3-Grb7-Erbb2-Stard3-Fbxl20 chromatin , we observed stress responses in the validated circadian chromatin 3D structure-regulated genes Nr1d2 , Npas2 , Rorc , and Pard3 . 8 , 21 , 22 , 31 , 35 , 41 , 42 NR1D1 downstream circadian gene Arntl ( Bmal1 ), Nfil3 elevated. 16 IBS therapeutic target homolog Slc9a3 (hydrogen exchanger 3 /Nhe3 ) decreased.…”

“…GR binding at these promoters and the WAS-induced Ikzf3 - Zpbp2 promoter E-box GR peak suggest long-range regulation in addition to the promoter activity ( Figure 4 A). 35 To clarify the effect of stress on chromatin 3D structures, we employed a high-accuracy BL-Hi-C method. 48 Furthermore, we compared the chromatin 3D structures with transcriptome and GR cistrome data.…”

“… 27 , 28 , 31 This SNP also regulates IBD DEGs encoded within the conserved 17q12-q21 ERBB2 ( HER2 ) -GRB7-IKZF3-ZPBP2-GSDMB-ORDML3-MED24 chromatin region upstream of NR1D1 and is associated with differential responses to GC therapy against asthma. 34 , 35 , 36 The asthma-risk variants rs4065275 ( ORMDL3 site) and rs12936231 ( ZPBP2 site) switch CTCF-binding sites that mediate pathological IKZF3-ORMDL3 to ZPBP2-ORMDL3 chromatin loop changes. 37 Thus, the 5′ ZPBP2-ORMDL3 region regulates 3′ NR1D1 circadian transcription in cis from long distances.…”

“… 37 Thus, the 5′ ZPBP2-ORMDL3 region regulates 3′ NR1D1 circadian transcription in cis from long distances. 35 The potential GR-mediated chromatin interactions linking these regulatory SNPs have translational potential in precision medicine against psychological mood and anxiety disorders and IBS. 2 , 23 , 30 In vitro germ-free colonoids used in the Capture-C sequencing study tend to lose circadian oscillatory transcription without daily GC treatments; it has limitations in studying intestinal epithelium Nr1d1 regulated by circadian and microbiota in vivo.…”