Mapping Replication Origins by Quantifying Relative Abundance of Nascent DNA Strands Using Competitive Polymerase Chain Reaction

Abstract

A procedure was developed for mapping origins of DNA replication in mammalian cell chromosomes based on determining the relative abundance of nascent DNA strands throughout a specific genomic region. The method entails purification of short strands of nascent DNA derived from recently activated origins and the quantification, within this sample, of the relative abundances of different adjacent DNA segments by a competitive polymerase chain reaction technique. It is expected that the abundance of defined markers within the origin region is greatest at the site where DNA replication begins. This origin mapping procedure (i) allows analysis of single-copy genomic regions, (ii) can be performed on cultured and primary cells in the absence of any chemical treatment, (iii) does not require cell synchronization, and (iv) allows mapping origins to within a few hundred base pairs. This high degree of resolution permits a study of thecis- andtrans-acting elements required for origin function. Application of this method to single-copy sequences in mammalian cells has identified replication origins within an ∼500-bp segment in the human lamin B2 gene domain and within an ∼800-bp segment in the hamster dihydrofolate reductase gene locus.