Additional file 11

AT1156 is an apparent exception to the general correspondence between detection of bubble arcs by 2D gel electrophoresis and replication above the detection threshold (relative copy number of 1.1) in our microarray studies. In this case, the AT island scored as “medium” in our microarray experiment (additional files 10-11) but did not display a bubble arc when tested by 2D gel electrophoresis of unsynchronized cells [1]. Panel A shows the microarray results for the region around AT1156. The two probes immediately flanking AT1156 are contained in the box. The evidence for AT1156 being a functional origin seems compelling. The probe on its left scored above threshold at both the 2-hr and 4-hr time points in all three tested strains, and AT1156 is within 6 kb of putative origins detected in both wild-type and cds1∆ cells by accumulation of ssDNA [2] and in wild-type cells by copy-number measurements [3]. In addition, an active pre-RC was detected by Hayashi et al. [4] at the position of AT1156 (Panel A). We suspect that in this case the 2D gel analysis failed for some reason to detect a bubble arc. This sometimes happens as a consequence of shearing during DNA preparation or due to single-strand-specific endonuclease contamination of the restriction enzyme. AT2103, which is also known as ars727, is another apparent exception. Previous 2D gel studies were not able to detect a bubble arc associated with ars727, yet this region was classified 5.25x10 6 5.24 5.23 5.22 Nucleotide Position Along Chromosome 1 2.0 1.5 1.0 2.0 1.5 1.0 0.5