New, easy, quick and efficient DNA replication timing analysis by high-throughput approaches

DNA replication must be faithful and follow a well-defined spatio-temporal program closely linked to genomic organization, transcription, epigenomic marks, intra-nuclear structures, mutation rate and cell fate determination. Replication timing (RT) analyses require complex, precise and time-consuming experimental procedures, and the study of large-size computer files. We improved the RT protocol to speed up and increase its quality and reproducibility. We partly automated the RT protocol via the IP-star robot (Diagenode) and developed a user-friendly software: the START-R suite (Simple Tool for the Analysis of the Replication Timing based on R). START-R suite is an open source software using an R script and an HTML interface to analyse DNA replication timing in a given cell line from microarray or deep-sequencing results. This new approach can be used by every biologist without specific knowledge in bioinformatics and reduces the time required for generating and analyzing data from several samples simultaneously. START-R suite detects constant timing regions (CTR) but also, and it is a novelty, it identifies temporal transition regions (TTR) and significant differences between two experimental conditions. The informatic global analysis requires less than 10 minutes. Nascent-DNA from early S-phase versus nascent-DNA from late S-phase.