CpG methylation has been linked to transcriptional regulation, genomic imprinting, and development. CpG methylation is tightly regulated during replication and differentiation of somatic cells. Alteration of methylation patterns has also been frequently observed in cancers. Although changes of methylation patterns during development and carcinogenis have been studied extensively, the mechanisms of the methylation changes have not been explored. Understanding of the impact and mechanism of DNA methylation could provide insights into human diseases recently found to be caused by mutations in methylation-related genes. It has been the goal of the investigators to dissect the impact of DNA methylation on transcription and the mechanism of demethylation utilizing the episomal system that they have developed in the past three years of the funding period. They have made important progress in the understanding of these events. In the next few years, they would like to continue to take advantage of this simplified system to test the following hypotheses: (1) Protein binding can protect sites from de novo methylation. (2) Methylation-mediated histone deacetylation is a local effect that only impacts the most immediate nucleosomes. (3) MeCP2 affects CpG poor and CpG rich DNA differently. They would also like to further investigate some of the same events and processes in the chromosomes using chromosomally integrated systems. This will allow direct comparison of the episomal and the integrated systems. If these events and processes are the same on the episome and in the chromosome, the episomal system can be used more aggressively to study methylation processes of endogenous genes. If differences in these two systems are found, the understanding of the basis of these differences will also provide insights regarding the dynamics of DNA methylation.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Mammalian Genetics Study Section (MGN)
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Carter, Anthony D
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University of Southern California
Schools of Medicine
Los Angeles
United States
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Okitsu, Cindy Yen; Hsieh, Chih-Lin (2007) DNA methylation dictates histone H3K4 methylation. Mol Cell Biol 27:2746-57
Irvine, Ryan A; Lin, Iping G; Hsieh, Chih-Lin (2002) DNA methylation has a local effect on transcription and histone acetylation. Mol Cell Biol 22:6689-96
Lin, Iping G; Han, Li; Taghva, Alexander et al. (2002) Murine de novo methyltransferase Dnmt3a demonstrates strand asymmetry and site preference in the methylation of DNA in vitro. Mol Cell Biol 22:704-23
Lin, I G; Hsieh, C L (2001) Chromosomal DNA demethylation specified by protein binding. EMBO Rep 2:108-12
Lin, I G; Tomzynski, T J; Ou, Q et al. (2000) Modulation of DNA binding protein affinity directly affects target site demethylation. Mol Cell Biol 20:2343-9
Hsieh, C L (1999) In vivo activity of murine de novo methyltransferases, Dnmt3a and Dnmt3b. Mol Cell Biol 19:8211-8
Hsieh, C L (1999) Evidence that protein binding specifies sites of DNA demethylation. Mol Cell Biol 19:46-56
Gauss, G H; Domain, I; Hsieh, C L et al. (1998) V(D)J recombination activity in human hematopoietic cells: correlation with developmental stage and genome stability. Eur J Immunol 28:351-8
Hsieh, C L (1997) Stability of patch methylation and its impact in regions of transcriptional initiation and elongation. Mol Cell Biol 17:5897-904