Replication dynamics of the yeast genome.

Oligonucleotide microarrays were used to map the detailed topography of chromosome replication in the budding yeast Saccharomyces cerevisiae. The times of replication of thousands of sites across the genome were determined by hybridizing replicated and unreplicated DNAs, isolated at different times in S phase, to the microarrays. Origin activations take place continuously throughout S phase but with most firings near mid-S phase. Rates of replication fork movement vary greatly from region to region in the genome. The two ends of each of the 16 chromosomes are highly correlated in their times of replication. This microarray approach is readily applicable to other organisms, including humans.

[1]  C. Rivin,et al.  Replication fork rate and origin activation during the S phase of Saccharomyces cerevisiae , 1980, The Journal of cell biology.

[2]  W. L. Fangman,et al.  A position effect on the time of replication origin activation in yeast , 1992, Cell.

[3]  Daniel R. Richards,et al.  Direct allelic variation scanning of the yeast genome. , 1998, Science.

[4]  S. Kearsey.  Structural requirements for the function of a yeast chromosomal replicator , 1984, Cell.

[5]  R. Hand.  Regulation of DNA replication on subchromosomal units of mammalian cells , 1975, The Journal of cell biology.

[6]  A Bensimon,et al.  Monitoring S phase progression globally and locally using BrdU incorporation in TK(+) yeast strains. , 2001, Nucleic acids research.

[7]  D. Gottschling,et al.  Telomeric chromatin modulates replication timing near chromosome ends. , 1999, Genes & development.

[8]  R. McCarroll,et al.  Time of replication of yeast centromeres and telomeres , 1988, Cell.

[9]  J. Diffley,et al.  The Cdc7 protein kinase is required for origin firing during S phase. , 1998, Genes & development.

[10]  E. Schwob,et al.  Think global, act local--how to regulate S phase from individual replication origins. , 2000, Current opinion in genetics & development.

[11]  F. Cross,et al.  CLB5-dependent activation of late replication origins in S. cerevisiae. , 1998, Molecular cell.

[12]  C. Newlon,et al.  Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III , 1990, Molecular and cellular biology.

[13]  R. Wellinger,et al.  Saccharomyces telomeres acquire single-strand TG1–3 tails late in S phase , 1993, Cell.

[14]  T. Canfield,et al.  Role of late replication timing in the silencing of X-linked genes. , 1996, Human molecular genetics.

[15]  J. Blow,et al.  The regulation of replication origin activation. , 1999, Current opinion in genetics & development.

[16]  W. L. Fangman,et al.  Multiple determinants controlling activation of yeast replication origins late in S phase. , 1996, Genes & development.

[17]  W. L. Fangman,et al.  Cdc7 is required throughout the yeast S phase to activate replication origins. , 1998, Genes & development.

[18]  W. L. Fangman,et al.  A yeast origin of replication is activated late in S phase , 1991, Cell.

[19]  K. H. Wolfe,et al.  Molecular evidence for an ancient duplication of the entire yeast genome , 1997, Nature.

[20]  A. Wolffe,et al.  Inheritance of chromatin states. , 1994, Developmental genetics.

[21]  H Yoshikawa,et al.  The efficiency and timing of initiation of replication of multiple replicons of Saccharomyces cerevisiae chromosome VI , 1997, Genes to cells : devoted to molecular & cellular mechanisms.

[22]  C. Newlon,et al.  Time of replication of ARS elements along yeast chromosome III , 1989, Molecular and cellular biology.

[23]  John J. Wyrick,et al.  Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast , 1999, Nature.

[24]  L. Johnston,et al.  Getting started: regulating the initiation of DNA replication in yeast. , 1997, Annual review of microbiology.

[25]  C. Newlon,et al.  The structure and function of yeast ARS elements. , 1993, Current opinion in genetics & development.

[26]  J. Warner,et al.  The economics of ribosome biosynthesis in yeast. , 1999, Trends in biochemical sciences.

[27]  W. L. Fangman,et al.  Replication profile of Saccharomyces cerevisiae chromosome VI , 1997, Genes to cells : devoted to molecular & cellular mechanisms.

[28]  P. Sharp,et al.  Regional base composition variation along yeast chromosome III: evolution of chromosome primary structure. , 1993, Nucleic acids research.

[29]  N R Cozzarelli,et al.  Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[30]  D. Natale,et al.  DNA helical stability accounts for mutational defects in a yeast replication origin. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[31]  C. Schildkraut,et al.  Replication program of active and inactive multigene families in mammalian cells , 1988, Molecular and cellular biology.

[32]  K. H. Wolfe,et al.  Updated map of duplicated regions in the yeast genome. , 1999, Gene.