Nucleic Acids Research Advance Access published online on September 9, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp727
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Gene Regulation, Chromatin and Epigenetics |
In vivo methylation of mtDNA reveals the dynamics of protein–mtDNA interactions
1Department of Cell Biology and Anatomy and 2Department of Neurology, University of Miami School of Medicine, Miami, FL 33136, USA
*To whom correspondence should be addressed. Tel: +1-305-243-5858; Fax: +1-305-243-3914; Email: cmoraes{at}med.miami.edu
Received July 3, 2009. Revised August 5, 2009. Accepted August 17, 2009.
To characterize the organization of mtDNA–protein complexes (known as nucleoids) in vivo, we have probed the mtDNA surface exposure using site-specific DNA methyltransferases targeted to the mitochondria. We have observed that DNA methyltransferases have different accessibility to different sites on the mtDNA based on the levels of protein occupancy. We focused our studies on selected regions of mtDNA that are believed to be major regulatory regions involved in transcription and replication. The transcription termination region (TERM) within the tRNALeu(UUR) gene was consistently and strongly protected from methylation, suggesting frequent and high affinity binding of mitochondrial transcription termination factor 1 (mTERF1) to the site. Protection from methylation was also observed in other regions of the mtDNA, including the light and heavy strand promoters (LSP, HSP) and the origin of replication of the light strand (OL). Manipulations aiming at increasing or decreasing the levels of the mitochondrial transcription factor A (TFAM) led to decreased in vivo methylation, whereas manipulations that stimulated mtDNA replication led to increased methylation. We also analyzed the effect of ATAD3 and oxidative stress in mtDNA exposure. Our data provide a map of human mtDNA accessibility and demonstrate that nucleoids are dynamically associated with proteins.