Figure 2

Microarray measurements of copy number increases on a segment of DNA in the right arm of chromosome 1. For clarity, the symbols used in this graph are explained in the keys (boxes) above and below the graph. They are also explained here. The information in this legend applies not only to Fig. 2 but also to Figs. 7 and 8, and to Additional Files 1, 2, 3 and 11, 12, 13, 14. The upper set of vertical lines shows relative copy numbers of the indicated probes 2 hrs after release from the G2 block, while the lower set of vertical lines shows results for 4-hr cells. Green lines: wild-type cells (JLP1164), plotted at their correct positions. Blue lines: cds1 Δ (JLP1257), plotted to the right of their correct positions. Red lines: rad3 Δ (JLP1260), plotted further to the right of their correct positions. The horizontal offsets of the blue and red lines were introduced to permit simultaneous visualization of the results for all three strains (wild-type, cds1 Δ and rad3 Δ). The heights of most lines represent the averages of 3–5 independent hybridizations to the same probe. Due to probe-specific experimental noise, for a few probes the number of successful hybridizations was only one or two. The average deviations of the individual hybridizations from the average value are indicated by appropriately colored small rectangles above and below the end point of each vertical line. For probes with only a single successful hybridization, no rectangle is shown. Because the probes mostly correspond to predicted gene locations, they are not uniformly spaced along the DNA. The names of the probes are indicated in black vertical type. In most cases, the names of the probes are the same as the names of the genes in which they are located. These genes are shown as thick yellow arrows above the corresponding probe names. The red, continuous graph indicates AT content in a sliding 500-bp window along the genome. Lower down, the names and locations of AT islands [20] are shown in magenta. The AT islands are numbered sequentially from left to right in each chromosome (except for a few cases where their chromosomal locations have been altered due to improved sequencing results since the original assignment of AT island names [20]). A "+" after the AT island name (not present in Fig. 2, but present at some locations in Figs. 7 and 9 and Additional File 13) indicates that a restriction fragment containing the AT island has been tested by 2D gel electrophoresis and found to have origin activity. If the origin associated with an AT island was previously studied and assigned a name, we show that name immediately after the "+". Conversely, a "-" after the AT island name (not present in Fig. 2, but present at a subset of locations in Additional Files 1, 2, 3 and 11) indicates that a restriction fragment containing the AT island failed to show origin activity by 2D gel electrophoresis. Below the AT island names are light blue circles, which indicate each of the 401 locations identified as "stronger origins" by Heichinger et al. [14]. Further down are purple and orange circles, which show the positions identified as origins by Feng et al. [34] using the ssDNA method, in wild-type or cds1 Δ cells, respectively. At the bottom of the graph are red and dark blue symbols, which are circles in the case of Fig. 2 but could also be squares (as in Fig. 8A, C). The red circles/squares indicate the positions of pre-RCs which were found to be active by BrdU incorporation and were classified as strong/early origins [15] The blue circles/squares indicate pre-RCs which did not score as active by BrdU incorporation and were classified as late/weak origins [15]. Circles indicate pre-RCs whose signal strength was the same in wild-type and cds1 Δ cells, while squares indicate pre-RCs whose signal strength was higher in cds1 Δ cells than in wild-type cells. The latter were considered to indicate checkpoint-restrained origins [15].