From lipid- and diabetes-associated DNA methylation at the SREBF1 locus to gene regulatory mechanisms
Final Report Abstract
Epigenome-wide association studies (EWAS) have associated several differentially methylated CpG sites to lipid levels. However, methylation-sensitive mechanisms underlying these signals remain elusive. Several CpG sites at the Sterol Regulatory Element Binding Transcription Factor 1 (SREBF1) locus are robustly associated with abnormal lipid levels and metabolic disorders. In this study we aimed to identify methylation-sensitive molecular mechanisms linked to lipidassociated CpG sites at the SREBF1 locus. We first prioritized lipid-associated SREBF1-CpG sites with strong potentially regulatory effects. Selected sites were further functionally assessed in Huh7, HepG2, HEK293, THP-1, and Jurkat cell lines. The differential protein binding of methylated CpG sites was assessed through electrophoretic mobility shift assays, while the transcriptional effect of methylated sites was tested through luciferase assays. Methylation-sensitive transcription factors were identified at cg11024682 through methylation-specific quantitative proteomics. Finally, an assessment of the link between methylation at the lipid-associated CpG sites with gene expression and lipid-related phenotypes was performed. Methylation at four CpG sites was associated with high lipid levels, which were carried forward for functional analysis. The four CpG-sites showed an increased expression at the methylatedstate of each CpG site, whereas only three showed methylation-sensitive protein binding across cell lines. Amongst the tested CpG sites, cg11024682 showed two methylation-specific protein bands replicated in two cell lines and the highest transcriptional effects across all cell lines. Methylation-specific transcription factors and cofactors differentially binding at cg11024682 included KDM2B, ATF7, MBD2, MeCP2, and SMARCAL1. In validation experiments only ATF7 showed differential binding and higher affinity to methylated-cg11024682. Further associations with lipoproteins showed three SREBF1-CpG sites to be mainly associated with the triglyceride content of both very low- and high-density lipoproteins. In summery we show, that DNA methylation at lipid associated-CpG sites within the SREBF1 locus increase gene transcription, with ATF7 is a methylation-specific transcription factor playing a key role. DNA methylation at SREBF1-CpG sites is associated with total lipid levels via specific lipid features of lipoprotein particles, pointing to cg11024682 as the one exerting the highest effects on the phenotype.
Publications
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DNA methylation in human lipid metabolism and related diseases. Current Opinion in Lipidology, 29(2), 116-124.
Mittelstraß, Kirstin & Waldenberger, Melanie
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A multi-ethnic epigenome-wide association study of leukocyte DNA methylation and blood lipids. Nature Communications, 12(1).
Jhun, Min-A.; Mendelson, Michael; Wilson, Rory; Gondalia, Rahul; Joehanes, Roby; Salfati, Elias; Zhao, Xiaoping; Braun, Kim Valeska Emilie; Do, Anh Nguyet; Hedman, Åsa K.; Zhang, Tao; Carnero-Montoro, Elena; Shen, Jincheng; Bartz, Traci M.; Brody, Jennifer A.; Montasser, May E.; O.’Connell, Jeff R.; Yao, Chen; Xia, Rui ... & Assimes, Themistocles L.
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DNA methylation and lipid metabolism: an EWAS of 226 metabolic measures. Clinical Epigenetics, 13(1).
Gomez-Alonso, Monica del C.; Kretschmer, Anja; Wilson, Rory; Pfeiffer, Liliane; Karhunen, Ville; Seppälä, Ilkka; Zhang, Weihua; Mittelstraß, Kirstin; Wahl, Simone; Matias-Garcia, Pamela R.; Prokisch, Holger; Horn, Sacha; Meitinger, Thomas; Serrano-Garcia, Luis R.; Sebert, Sylvain; Raitakari, Olli; Loh, Marie; Rathmann, Wolfgang; Müller-Nurasyid, Martina ... & Waldenberger, Melanie
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Meta-analysis of epigenome-wide association studies of carotid intima-media thickness. European Journal of Epidemiology, 36(11), 1143-1155.
Portilla-Fernández, Eliana; Hwang, Shih-Jen; Wilson, Rory; Maddock, Jane; Hill, W. David; Teumer, Alexander; Mishra, Pashupati P.; Brody, Jennifer A.; Joehanes, Roby; Ligthart, Symen; Ghanbari, Mohsen; Kavousi, Maryam; Roks, Anton J. M.; Danser, A. H. Jan; Levy, Daniel; Peters, Annette; Ghasemi, Sahar; Schminke, Ulf; Dörr, Marcus ... & Dehghan, Abbas
