Up and down the slope: Replication timing and fork directionality gradients in eukaryotic genomes

Abstract

Modern techniques allow the genome-wide determination of the replication time (RT) of any sequence in eukaryotic cell populations. Because origin firing is stochastic, the mean replication time (MRT) of a locus in a cell population depends on the firing time probability distribution of both neighboring and distant origins as well as on replication fork progression rates. Interpreting MRT profiles in terms of origin firing is therefore delicate. Theory predicts a simple relationship between the derivative (slope) of MRT profiles, the speed of replication forks, and the proportions of rightward- and leftward-moving forks replicating that locus (replication fork directionality; RFD). RFD profiles have been obtained by several independent methods: derivative of MRT profiles; nucleotide compositional skew analysis; sequencing of purified Okazaki fragments; and analysis of biased ribonucleotide incorporation in the two strands of the DNA. Using mathematical models, both MRT and RFD profiles allow quantitative inferences about the location and timing of replication initiation and termination events genome-wide. We summarize results and models of the replication program obtained by these approaches and their potential links with replication foci, chromatin states, and globular chromosomal domains.