title: DNA replication initiates at different sites in early and late S phase within human ribosomal RNA genes.
abstract: Metazoan replication origins often contain multiple potential initiation sites, and the selection of which of the potential sites are used appears to be dependent upon multiple factors, including the state of differentiation, cell metabolism, and local transcriptional activity. Numerous studies have shown that a replication origin exists within the non-transcribed spacer region of the human ribosomal RNA gene. We here analyze nascent leading strand DNA from S phase human lymphoid cells, and find that while the majority of rDNA replicates in mid- and late S phase and preferentially initiates replication 6 kbp from the transcription start site, in very early S phase the preferred initiation site is much closer to the transcription start site and may involve rDNA promoter sequences. This early site is coincident with a minimum GC skew value, diagnostic for replication origins in bacteria and yeast. These results suggest that replication timing can influence initiation site selection. The timing and nucleolar localization of rDNA further suggest that this site likely participates in the small number of perinucleolar initiation foci observed in very early S phase cells that represent the beginning of cellular DNA replication.
authors.affiliation: Department of Pathology and Laboratory Medicine, UMDNJ-New Jersey Medical School, Newark, New Jersey 07103, USA. coffmafd@umdnj.edu
authors.forename: Frederick D
authors.initials: FD
authors.lastname: Coffman
authors.forename: Mai
authors.initials: M
authors.lastname: He
authors.forename: Mai-Ling
authors.initials: ML
authors.lastname: Diaz
authors.forename: Stanley
authors.initials: S
authors.lastname: Cohen
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000502:physiology; D001665:Binding Sites; D045744:Cell Line, Tumor; D002466:Cell Nucleolus / Q000378:metabolism; D002469:Cell Separation; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D017931:DNA Primers / Q000737:chemistry; D004261:DNA Replication; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D021903:DNA, Ribosomal Spacer; D005347:Fibroblasts / Q000378:metabolism; D005434:Flow Cytometry; D005656:Fungal Proteins / Q000502:physiology; D006801:Humans; D008214:Lymphocytes / Q000378:metabolism; D016133:Polymerase Chain Reaction; D011419:Propidium / Q000494:pharmacology; D012335:RNA, Ribosomal / Q000235:genetics*; D018741:Replication Origin; D016196:S Phase; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D017931:DNA Primers; D004275:DNA, Ribosomal; D021903:DNA, Ribosomal Spacer; D005656:Fungal Proteins; D012335:RNA, Ribosomal; D011419:Propidium; D004247:DNA