Replication characteristics determined by high-throughput sequencing.

<p><b>A</b>. Base-pair frequency gradients. Data points are averages of binned read numbers representing successive blocks of 10kbp for c1 and c2 and 1kbp for c3. The top panels show the raw data for DNA from exponentially-growing cells, the third row shows the same data after division by the correspondingly binned data obtained from stationary-phase cells (second row). Nucleotide positions on the abscissa are reversed to conform to the intuitive sense of right and left chromosome arms. Because the data are plotted as raw read frequencies, relative copy numbers of the replicons can be read from the ordinates. <b>B</b>. Calculation of chromosome replication period, C, and speed. Origin/terminus ratios were used to calculate the time taken to replicate each chromosome arm from <i>ori</i>/<i>ter</i> = 2^C/τ. In the case of c1 and c2, the concavity of the stationary-phase base-pair frequency curves would falsify calculation of origin/terminus ratios from normalized data, necessitating use of the raw data plot. For this, raw data <i>ori</i>- and <i>ter</i>-proximal points that corresponded to points intersected by the linear regression plot of the normalized data were connected by lines whose upper extremities and intersection were taken as the <i>ori</i> and <i>ter</i> values respectively. The c3 stationary-phase bp frequency curve is essentially flat, validating the normalized data. The * values for c3 replication speed are calculated on the basis of terminus displacement creating arms estimated to be 340 and 530 kb long.