The gastrula transition reorganizes replication origin selection in Caenorhabditis elegans

Some features underlying replication origin activation in metazoan cells have been identified, but little is known about their regulation during metazoan development. Using the nascent strand purification method, we identified replication origins throughout Caenorhabditis elegans embryonic development and found that the origin repertoire is thoroughly reorganized after gastrulation onset. During the pluripotent embryonic stages (pre-gastrula), potential cruciform structures and open chromatin are determinant factors to establish replication origins. The enrichment of replication origins in transcription factor binding sites and their presence inside promoters of highly transcribed genes, particularly operons, argue that transcriptional activity contributes to replication initiation before gastrulation. After the gastrula transition, when differentiation programs are set in the embryos, origins are particularly selected at enhancers, in the vicinity of CGI-like sequences, and non-coding genes. Our findings suggest that origin selection coordinates replication initiation with transcriptional programs during metazoan development. 3 replicates for pre-gastrula embryos and 3 for mixed embryos are analyzed. A replicate of L1 negative control is used for identification of the specific signal by subtracting it from the samples, and RNase treated control is generated as a technical control for the procedure used to identify replication origins. Please note that [1] a description of each data column (in the processed data *txt files) is provided in the 'readme.txt' and [2] the column 'M.norm.minus.neg.w5' contains the data that forms the basis of this study's conclusion.