Delving into Eukaryotic Origins of Replication Using DNA Structural Features

DNA replication in eukaryotes is an intricate process, which is precisely synchronized by a set of regulatory proteins, and the replication fork emanates from discrete sites on chromatin called origins of replication (Oris). These spots are considered as the gateway to chromosomal replication and are stereotyped by sequence motifs. The cognate sequences are noticeable in a small group of entire origin regions or totally absent across different metazoans. Alternatively, the use of DNA secondary structural features can provide additional information compared to the primary sequence. In this article, we report the trends in DNA sequence-based structural properties of origin sequences in nine eukaryotic systems representing different families of life. Biologically relevant DNA secondary structural properties, namely, stability, propeller twist, flexibility, and minor groove shape were studied in the sequences flanking replication start sites. Results indicate that Oris in yeasts show lower stability, more rigidity, and narrow minor groove preferences compared to genomic sequences surrounding them. Yeast Oris also show preference for A-tracts and the promoter element TATA box in the vicinity of replication start sites. On the contrary, Drosophila melanogaster, humans, and Arabidopsis thaliana do not have such features in their Oris, and instead, they show high preponderance of G-rich sequence motifs such as putative G-quadruplexes or i-motifs and CpG islands. Our extensive study applies the DNA structural feature computation to delve into origins of replication across organisms ranging from yeasts to mammals and including a plant. Insights from this study would be significant in understanding origin architecture and help in designing new algorithms for predicting DNA trans-acting factor recognition events.