Nucleotide skew and GC-rich elements at replication origins. (A) Origins were centered on Drosophila CGI-like regions. The mean AT and GC percentages of centered Oris are shown. Genome-scale NS signal strengths are represented by a black line. Note that the NS peaks (putative replication initiation sites) are not enclosed in the central CG-rich region. (B) Genome-scale nucleotide distribution of all Drosophila origins centered on the NS peak. Note the skew in nucleotide distribution with GT and AC enrichment at the 5′ and 3′ end of the origin peak, respectively. (C) Nucleotide distribution at and around the origin peak for origins in Drosophila Kc cells; 200 bp sequences of 300 replication origins were stacked and aligned around the NS peak. Four colors were used: green for A, red for T, yellow for G, and blue for C. The exact sequence can be read by enlarging the figure in Supplemental Data. A clear bias is observed for C or G, and A or T around the NS peak. (D) Motifs frequently found in Drosophila (top panel) and mouse (bottom panel) replication origins. The E-value is indicated (see Methods).
