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Fig. 1. Abf2 associates preferentially with complex GC-rich sequences. (A) Southern blot hybridizations of blots of mtDNA digested with DraI with the following probes: CsCl-purified total mtDNA sheared by sonication (left panel), DNA coimmunoprecipitated with an anti-Myc antibody from the strain expressing Abf2-13Myc fusion protein (middle panel), and DNA coimmunoprecipitated with an anti-Myc antibody from the control strain expressing untagged Abf2 (right panel). (B) The median-percentile rank analysis of ChIP DNA microarray hybridizations (supplementary material Fig. S3). All data points were sorted from highest to lowest Cy5:Cy3 ratios and each data point was assigned a percentile rank. The median-percentile ranks of each mtDNA region from three Abf2-13Myc and four Abf2 ChIP experiments were compared by subtracting the control medians (Abf2) from the sample medians (Abf2-13Myc). The gray peak represents the median-percentile rank difference of all mtDNA regions examined with the microarrays. The dark-gray peak shows median-percentile ranks of all the complex GC-rich sequences in the dataset; a bias to higher median-percentile ranks is evident. Therefore, these sequences were enriched in Abf2-13Myc ChIP sample. (C) A list of all DNA spots consistently enriched in the Abf2-13Myc ChIP-chip experiments. (D) Circular map of the intronless mtDNA. The inner black markers identify sequences covered by mtDNA microarray analysis. The innermost gray markers identify the regions significantly enriched in the Abf2-13Myc ChIP-chip experiments.
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