Supplementary Figure 6: Sequence motifs associated with replication origins.
From: The gastrula transition reorganizes replication-origin selection in Caenorhabditis elegans
Scanning for the occurrence of GCTAAAA (a), [AC][GC]GC[CG]C (b) and CG[AC][GC]GCGC (c) motifs in 1-kb regions on both sides of origin summits. The x-axis indicates the position relative to the origin summit, the y-axis the percentage of pre-gastrula origins (green line), post-gastrula-specific origins (orange line) or 100 randoms (gray lines) with at least one occurrence per 100-bp window. Both Watson (sense) and Crick (antisense) chromosomal strands were considered. (d) Box plots showing the total percentage of pre-gastrula (green) and post-gastrula-specific (orange) origin summits overlapping with CGI-like sequences (for origins and random data) (mean ± s.d.) and in (e) chromosome arms and center, separately. *, P<10-8 (according to the distribution function of the normal distribution). (f) Results of bubble trap and 2D gel electrophoresis analysis for a region containing a post-gastrula-specific origin with a CGI-like (positive region; brown box; left panels) and a region without origin and CGI-like (negative region; right panel, same negative region already shown in Figure 2C). The raw data of these regions are on top (combination of three NS microarray replicates), the qPCR validation in the middle, and the 2D gels at the bottom. The black box indicates the position of the probe used for hybridization and the thin pink lines, the Cla1 sites. The results at the bottom are shown for both regions, comparing a mixed embryo sample and a negative control (L1-arrested larval sample). The arrow indicates the position of the signal representing the replication origin.
