We have been studying epigenetics since the 1970’s. In collaboration with Charles Gehrke, we published the first study demonstrating tissue-specific differences in the levels of DNA methylation in humans. In 1983, our lab and, independently, the lab of Bert Vogelstein were the first to publish that there are abnormalities in DNA methylation in human cancers. Later, we were the first to report very frequent hypomethylation of highly repeated DNA sequences in human cancers. Our findings on genome-wide, cancer-associated DNA hypomethylation have been confirmed by numerous laboratories.
Our interest in how certain transcription factors might distinguish between methylated and nonmethylated DNA recognition sites led to the first report of a vertebrate DNA-binding protein with specificity for DNA methylation (MDBP/RFX). Alongside our many studies of this protein, we continued analyzing aberrant DNA hypermethylation vs. hypomethylation in human cancer, e.g., and the relationships between cancer-associated DNA hypomethylation and pericentromeric chromosome rearrangements. We also investigated this relationship in normal chorionic villus cultures. As a follow-up to studying the associations between DNA hypomethylation and chromosomal rearrangements, we studied a rare DNA methyltransferase deficiency (immunodeficiency, centromeric region instability, facial anomalies, ICF) in which there are bizarre diagnostic rearrangements of hypomethylated satellite DNA in the pericentromic regions of chromosomes 1 and 16.
Results from our research on additional targets of abnormal DNA hypomethylation in the ICF syndrome converged with our earlier findings of sequences displaying gamete-associated DNA hypomethylation. One of the most interesting sequences that we found to display hypomethylation in ICF cells was a macrosatellite repeat sequence (D4Z4) that is associated with a very unusual type of dominant muscular dystrophy (facioscaulohumeral muscular dystrophy, FSHD). D4Z4 is very similar to a sequence with sperm-specific DNA hypomethylation that we had previously cloned.
We profiled genome-wide expression in myoblasts and myotubes from controls and FSHD patients to better understand normal and aberrant muscle formation. In that study we uncovered the first convincing evidence for generalized dysregulation of gene expression in this disease. Our study indicates the underappreciated complexity of the role of D4Z4 hypomethylation in FSHD.
To better understand transcription control in FSHD and other muscular dystrophies as well as in aging and cachexia, we characterize genome-wide epigenetic changes associated with myogenesis and postnatal skeletal muscle using ENCODE and RoadMap whole-genome profiles of human DNA methylation and chromatin epigenetic marks in myogenic progenitor cells, skeletal muscle tissue, and many different types of samples. Among the genes we studied in detail for their relationships between skeletal muscle lineage-specific epigenomics (including DNA hydroxymethylation) and transcriptomics were the early differentiation-linked HOX genes, ubiquination-associated ASB family genes and KLHL family genes , and Notch-signaling genes. These studies provided new insights into the variety of transcription modulatory roles played by differential DNA methylation, intragenic enhancers, and distant intergenic enhancers. For example, we described evidence for dual-purpose enhancers that upregulate expression of the gene in which they reside in one cell type and upregulate an adjacent gene in another cell type.
In one of a series of reporter gene studies, we targeted in vitro DNA methylation to myoblast-hypermethylated enhancer or promoter elements and demonstrated that methylation of as little as three clustered CpGs could repress a potent MYOD1 enhancer element. From other reporter gene assays coupled with in vivo bioinformatics, we provided evidence that tissue-specific DNA methylation at some 5’ gene regions can down-modulate cell type-specific transcription rather than silence it. Our analyses of the effects of DNA hypermethylation on gene expression includes our ongoing interest in cancer-associated DNA hypermethylation.
Our research on developmental epigenetic changes has recently expanded to include heart and aorta and their associated diseases. We recently discovered tissue-specific expression-linked super-enhancers at five genes that are critical for cardiac fibrosis . From another bioinformatic study of atherosclerotic vs. control aorta methylomes, we provided evidence for atherosclerosis-linked DNA methylation changes in aorta that might help minimize or reverse the standard contractile character of many of these cells by abnormally down-modulating smooth muscle-related enhancers. We are also currently using in-depth tissue-comparative bioinformatics to inform analysis of genetic variants identified in genome-wide association studies (GWAS) of osteoporosis and obesity traits.
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