Fig. 3

In vivo and in silico functional analysis of ARID5B CpG cg25953130. a ARID5B mRNA expression (y axis; normalized value) is significantly negatively correlated (Pearson’s r) with methylation of a CpG (cg25953130) in 1264 CD14+ samples from MESA participants. b A regional association plot of ARID5B CpG methylation with carotid plaque score in MESA (y axis: −log₁₀ (p-value), x axis: position on chromosome (chr) 10) is shown in the top panel; the bottom panel shows the ARID5B expression-associated CpG (cg25953130, chr10:63,753,550, hg19, indicated by the light blue line) located in an ARID5B intron, overlaps a DNase hypersensitive site in a CD14+ sample from BLUEPRINT, histone marks indicative of a strong enhancer/promoter in a CD14+ and B-cell line sample from BLUEPRINT and ENCODE (see Supplementary Fig. 3 for ChromHMM color code), as well as a transcription factor binding site for EP300, detected in a neuroblastoma cell line (SK-N-SH_RA). c A physical interaction is detected between the ARID5B promoter and the region near the ARID5B CpG cg25953130 by both HiC and ChIA-PET data. The heatmap (white, low; red, high; top panel) graphically displays Hi-C interaction counts (the normalized number of contacts between a pair of loci) for the large region surrounding ARID5B in a B-cell line (GM12878; reported by Rao et al.³⁹); active enhancer marks (H3K27ac and H3K4me1 in GM12878 from ENCODE) are shown below; the bottom panel zooms in on ARID5B (blue highlighted region) Hi-C interaction. There were 1,937 contacts between the ARID5B promoter and the cg25953130 region. Below the Hi-C interaction is a depiction of detected ChIA-PET interactions (chromatin interaction analysis by paired-end tag sequencing) for the region flanking ARID5B in the B-cell line (GM12878; reported by Heidari et al.⁴¹), represented by blue curves