Addional Figure 1. Chromatin and Replication Protein Architecture at 217 Fission Yeast DNA Replication Origins.

Link to PDF file

Each page of this multi-page PDF file displays chromatin architecture and abundance of pre-RC proteins in a 4-kb window centered on a single replication origin. The 217 origins were selected because (a) they had previously been identified as both AT islands (Segurado et al, 2003; Mickle et al., 2007) and peaks of pre-RC proteins (Hayashi et al., 2007; see main text for full reference details), and the AT island peak position was within 500 bp of the pre-RC peak position, and (b) enough of the region was mappable (no repeated sequences) to permit accurate calculation of chromatin profiles and pre-RC protein distributions near the origin. The origins are arranged according to their positions along the chromosome, in chromosome order. Thus the first origin (corresponding to AT1011) is at the left end of chromosome 1, and the last origin (corresponding to AT3068) is at the right end of chromosome 3.

For each origin, panels (i) through (iv) of Additional Figure 1 correspond to panels (i) through (iv) in Figure 4 and in Supplementary Figure S5 of the main text. The legends for those figures accurately describe panels (i) through (iv) in Additional Figure 1. However, panel (v) of Additional Figure 1 differs somewhat from, and is more informative than, panels (v) of Figure 4 and Supplementary Figure S5 of the main text.

For Additional Figure 1, panel (v): The 3' ends of genes (coding sequences) are shown with green vertical lines; the 5' ends of genes are shown with red vertical lines. Gene names are indicated with black vertical type, centered between gene ends. Transcriptional start sites (TSSs) are shown with green angle signs (> or <, depending on the direction of transcription). Transcriptional termination sites (TTSs) are indicated by red angle signs. AT island names are shown at positions of peak AT content with magenta vertical type. Pre-RC protein peaks (as judged by Hayashi et al., 2007) are shown with small solid squares or circles. These are colored red if the origin was judged by Hayashi et al., 2007, to be strong or early; they are colored blue if the origin was judged to be weak or late. Circles indicate origins whose signal strength was essentially the same in wild-type and cds1-delta (checkpoint-deficient) cells, while squares indicate origins whose signal strength was significantly higher in cds1-delta cells than in wild-type cells (Hayashi et al., 2007). The colored characters, "+" and "-" near the top center of each panel (v) indicate the positions of the origin centers determined by ArchAlign software (Lai and Buck, 2010) for each of our samples: red, LFB; orange, LFN; green, LUN; blue, SUN. A "+" means that ArchAlign found that, for optimal alignment of that sample, the orientation of that particular origin should be the same as the chromosomal orientation. A "-" indicates that the origin orientation should be opposite to chromosomal. Similarly, the "L" and "R" characters show the origin centers determined when aligning origins by eye (see Materials and Methods in the main text). "R" means chromosomal orientation, and "L" means anti-chromosomal orientation.