Liver X Receptor–Binding DNA Motif Associated With Atherosclerosis‐Specific DNA Methylation Profiles of <i>Alu</i> Elements and Neighboring CpG Islands

Background The signals that determine atherosclerosis‐specific DNA methylation profiles are only partially known. We previously identified a 29‐bp DNA motif (differential methylation motif [ DMM] ) proximal to CpG islands ( CGI s) that undergo demethylation in advanced human atheromas. Those data hinted that the DMM docks modifiers of DNA methylation and transcription. Methods and Results We sought to functionally characterize the DMM . We showed that the DMM overlaps with the RNA polymerase III –binding B box of Alu short interspersed nuclear elements and contains a DR 2 nuclear receptor response element. Pointing to a possible functional role for an Alu DMM , CGI s proximal (&lt;100 bp) to near‐intact DMM –harboring Alu are significantly less methylated relative to CGI s proximal to degenerate DMM –harboring Alu or to DMM ‐devoid mammalian‐wide interspersed repeat short interspersed nuclear elements in human arteries. As for DMM ‐binding factors, LXRB (liver X receptor β) binds the DMM in a DR 2‐dependent fashion, and LXR (liver X receptor) agonists induce significant hypermethylation of the bulk of Alu in THP ‐1 cells. Furthermore, we describe 3 intergenic long noncoding RNA s that harbor a DMM , are under transcriptional control by LXR agonists, and are differentially expressed between normal and atherosclerotic human aortas. Notably, CGI s adjacent to those long noncoding RNA s tend to be hypomethylated in symptomatic relative to stable human atheromas. Conclusions Collectively, the data suggest that a DMM is associated with 2 distinct methylation states: relatively low methylation of in cis CGI s and Alu element hypermethylation. Based on the known atheroprotective role of LXR s, we propose that LXR agonist–induced Alu hypermethylation, a landmark of atherosclerosis, is a compensatory rather than proatherogenic response.