Altered methylation of specific DNA loci in the liver of Bhmt‐null mice results in repression of Iqgap2 and F2rl2 and is associated with development of preneoplastic foci

Abstract

Folate B₁₂-dependent remethylation of homocysteine is important, but less is understood about the importance of the alternative betaine-dependent methylation pathway-catalyzed by betaine-homocysteine methyltransferase (BHMT)-for establishing and maintaining adequate DNA methylation across the genome. We studied C57Bl/6J <i>Bhmt</i> (betaine-homocysteine methyltransferase)-null mice at age 4, 12, 24, and 52 wk (<i>N</i> = 8) and observed elevation of <i>S</i>-adenosylhomocysteine concentrations and development of preneoplastic foci in the liver (increased placental glutathione <i>S</i>-transferase and cytokeratin 8-18 activity; starting at 12 wk). At 4 wk, we identified 63 differentially methylated CpGs (DMCs; false discovery rate < 5%) proximal to 81 genes (across 14 chromosomes), of which 18 were differentially expressed. Of these DMCs, 52% were located in one 15.5-Mb locus on chromosome 13, which encompassed the <i>Bhmt</i> gene and defined a potentially sensitive region with mostly decreased methylation. Analyzing Hybrid Mouse Diversity Panel data, which consisted of 100 inbred strains of mice, we identified 97 DMCs that were affected by <i>Bhmt</i> genetic variation in the same region, with 7 overlapping those found in <i>Bhmt</i>-null mice (<i>P</i> < 0.001). At all time points, we found a hypomethylated region mapping to <i>Iqgap2</i> (IQ motif-containing GTPase activating protein 2) and <i>F2rl2</i> (proteinase-activated receptor-3), 2 genes that were also silenced and underexpressed, respectively.-Lupu, D. S., Orozco, L. D., Wang, Y., Cullen, J. M., Pellegrini, M., Zeisel, S. H. Altered methylation of specific DNA loci in the liver of <i>Bhmt</i>-null mice results in repression of <i>Iqgap2</i> and <i>F2rl2</i> and is associated with development of preneoplastic foci.