Control of DNA replication is critical to ensure accurate copy number of genes, because both loss of gene copies and increased copy number by amplification are associated with the onset of cancer and progression to metastatic states. Elucidation of regulatory mechanisms for metazoan DNA replication has been hampered by difficulty in defining specific origins of replication and monitoring their activation. Most animals, including humans, contain polyploid tissues in which the DNA content of the cells is increased by a modified cell cycle, the endo cycle, lacking mitosis. In addition to the overall increase in genomic DNA, in many polyploid cells differential DNA replication occurs in which specific genomic intervals are not replicated or in some cases are over-replicated and amplified. These instances of differential DNA replication provide superb models for elucidating the structure and regulation of metazoan DNA replication origins. Using genomic methodologies, amplified genomic regions were identified in the Drosophila ovarian follicle cells and single copy, euchromatic underreplicated regions were found in the larval salivary gland. The replication origins within the amplified regions are subject to developmental control and permit analysis of the factors responsible for origin activation and repression, as well as discovery of mechanisms by which metazoan DNA replication is initiated. The aims of this research are to exploit these Drosophila replication models to define the mechanisms that activate initiation at the origins during follicle cell differentiation, to determine how replication origins are inactivated and to use mutants to identify new regulatory proteins, and to analyze mechanisms controlling replication fork progression. The identification of defined replication origins whose duplication can be quantified, the ability to detect replication proteins bound at these origins and moving with the replication forks, combined with a collection of mutants affecting these processes permits these experimental goals to be achieved.