Efficient, quick and easy-to-use DNA replication timing analysis with START-R suite

Djihad Hadjadj (1) , Thomas Denecker (2) , Eva Guérin (1) , Su-Jung Kim (1) , Fabien Fauchereau (1) , Giuseppe Baldacci (1) , Chrystelle Maric (1) , Jean-Charles Cadoret (1)

1 IJM (UMR_7592) - Institut Jacques Monod
2 I2BC - Institut de Biologie Intégrative de la Cellule

DNA replication must be faithful and follow a well-defined spatiotemporal program closely linked to transcriptional activity, epigenomic marks, intranu-clear structures, mutation rate and cell fate determination. Among the readouts of the spatiotemporal program of DNA replication, replication timing analyses require not only complex and time-consuming experimental procedures, but also skills in bioinfor-matics. We developed a dedicated Shiny interactive web application, the START-R (Simple Tool for the Analysis of the Replication Timing based on R) suite, which analyzes DNA replication timing in a given organism with high-throughput data. It reduces the time required for generating and analyzing simultaneously data from several samples. It automatically detects different types of timing regions and identifies significant differences between two experimental conditions in ∼15 min. In conclusion, START-R suite allows quick, efficient and easier analyses of DNA replication timing for all organisms. This novel approach can be used by every biologist. It is now simpler to use this method in order to understand, for example, whether 'a favorite gene or protein' has an impact on replication process or, indirectly, on ge-nomic organization (as Hi-C experiments), by comparing the replication timing profiles between wild-type and mutant cell lines.

Domaines: Sciences du Vivant [q-bio]; Bio-Informatique, Biologie Systémique [q-bio.QM]; Biochimie, Biologie Moléculaire

Djihad Hadjadj, Thomas Denecker, Eva Guérin, Su-Jung Kim, Fabien Fauchereau, et al.. Efficient, quick and easy-to-use DNA replication timing analysis with START-R suite. NAR Genomics and Bioinformatics, 2020, 2 (2), ⟨10.1093/nargab/lqaa045⟩. ⟨hal-02929259⟩