Regulation of DNA replication during development

Abstract

As development unfolds, DNA replication is not only coordinated with cell proliferation, but is regulated uniquely in specific cell types and organs. This differential regulation of DNA synthesis requires crosstalk between DNA replication and differentiation. This dynamic aspect of DNA replication is highlighted by the finding that the distribution of replication origins varies between differentiated cell types and changes with differentiation. Moreover, differential DNA replication in some cell types can lead to increases or decreases in gene copy number along chromosomes. This review highlights the recent advances and technologies that have provided us with new insights into the developmental regulation of DNA replication.

Fig. 1.

Helicase loading (pre-RC assembly) and activation. (A) Helicase loading (pre-RC assembly) at a potential origin of replication coinciding with a transcription start site (arrow). Although origins are sequence independent in metazoans, histone modifications are associated with transcriptional activation, and open/active chromatin correlates with ORC binding. Histone modifications associated with repressive chromatin are negatively associated with ORC binding. During helicase loading, binding of the ORC complex promotes recruitment of Cdc6, which in turn promotes the loading of a Cdt1–Mcm2-7 double hexamer. (B) Kinase activation. DDK promotes helicase activation by phosphorylating multiple Mcm subunits. S-CDK promotes helicase activation by phosphorylating Sld2 and Sld3, which in turn allow the recruitment of additional factors necessary for helicase activation. (C) Helicase activation is dependent on the recruitment of additional factors necessary to activate the replicative Mcm2-7 helicase, which is a complex of Mcm2-7, Cdc45 and GINS proteins (Sld5, Psf1, Psf2 and Psf3). Arrows indicate the direction of helicase movement.

Fig. 2.

Replication domains encompass numerous potential origins of replication. (A) Replication timing experiments monitor changes in gene copy number or new DNA synthesis during multiple intervals of S phase, defining zones of early or late replication. Typically, cells can be separated into early (green box) and late (pink box) replication fractions based on their DNA content. DNA isolated from each fraction can be labeled and hybridized to a microarray, or directly sequenced to monitor copy number changes during S phase. (B) Replication domains typically extend from 200 kb to 2 Mb in size, encompassing numerous individual origins of replication (diagram shows the pre-RC as illustrated in Fig. 1). Consequently, population-scale replication timing experiments lack the resolution to monitor changes in individual origin usage during differentiation.

Fig. 3.

Differential DNA replication. (A) A mitotic cycle with four distinct phases: G1, S, G2 and M phase. (B) By contrast, the endo cycle consists of repeated rounds of S and G phases with no intervening mitoses, resulting in polyploid cells with increased genome content per cell. (C) Developmentally programmed gene amplification can occur through repeated rounds of origin firing followed by bidirectional replication fork progression, resulting in gradients of copy number over a 100 kb domain. The example shown depicts four rounds of origin firing. Arrows at top indicate direction of fork progression. (D) Schematic of the copy number differences associated with under-replication. Arrows at top indicate direction of fork progression relative to the maximally under-replicated region. Under-replicated domains within euchromatin range from 100 to 400 kb.