Functional analysis of in vivo and in organello footprinting of HeLa cell mitochondrial DNA in relationship to ATP and ethidium bromide effects on transcription. JBiolChem272

In vivo and in organello footprinting techniques based on methylation interference have been utilized to inves-tigate protein-DNA interactions in the transcription ini-tiation and rDNA transcription termination regions of human mitochondrial DNA (mtDNA) in functionally ac-tive mitochondria. In particular, the changes in methyl-ation reactivity of these regions in response to treat-ment of the organelles with ATP or ethidium bromide, which affects differentially the rates of mitochondrial rRNA and mRNA synthesis, have been analyzed. Two major sites of protein-DNA interactions have been iden-tified in the main control region of mtDNA, both in vivo and in organello, which correspond to the regions of the light-strand promoter and heavy-strand rRNA-specific promoter. The in organello footprinting of the latte