Genome-wide 5mC methyltransferase specificity detection in B. halodurans. The Circos plots show the genome-wide view of IPD ratios for (a) untreated and (b) mTet1-treated samples, with the outer and inner circle denoting the forward and reverse DNA strands, respectively. The IPD ratios of the +2 position in 5'-GGCC-3' sequence contexts are plotted in red, while IPD ratio data for all other contexts is plotted in grey. The graphs on the right show base-resolution IPD ratio views of a section of the genome containing two target sites for cytosine methylation (5'-GGCC-3'). (c) Kinetic score distributions before and after Tet1 conversion for all +2 positions of 5'-GGCC-3' in the genome. An orthogonal off-target motif (5'-CCGG-3') is also shown which was used to set a 1% false discovery rate threshold (dashed line, see methods for details) for tabulation of detected methylated positions (Table 1). The blue tick marks in the Circos plots of (a) and (b) denote 5'-GGCC-3' genomic positions detected as methylated using that threshold. 5mC: 5-methylcytosine; 6mA: 6-methyladenine; IPD: interpulse duration; mTet1: mouse Tet1.
Clark et al. BMC Biology 2013 11:4 doi:10.1186/1741-7007-11-4