Global organization of replication time zones of the mouse genome.

The division of genomes into distinct replication time zones has long been established. However, an in-depth understanding of their organization and their relationship to transcription is incomplete. Taking advantage of a novel synchronization method ("baby machine") and of genomic DNA microarrays, we have, for the first time, mapped replication times of the entire mouse genome at a high temporal resolution. Our data revealed that although most of the genome has a distinct time of replication either early, middle, or late S phase, a significant portion of the genome is replicated asynchronously. Analysis of the replication map revealed the genomic scale organization of the replication time zones. We found that the genomic regions between early and late replication time zones often consist of extremely large replicons. Analysis of the relationship between replication and transcription revealed that early replication is frequently correlated with the transcription potential of a gene and not necessarily with its actual transcriptional activity. These findings, along with the strong conservation found between replication timing in human and mouse genomes, emphasize the importance of replication timing in transcription regulation.

• Publication year

  2008

• Venue

  Genome Research

• Publication date

  2008-10-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1101/gr.079566.108PMID 18669478PMCID PMC2556267
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Gimme a Break!

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  2005cited by this paper
• Novel and quantitative DNA dot-blotting method for assessment of in vivo proliferation.

  2005cited by this paper
• Temporal profile of replication of human chromosomes.

  2005influential reference
• Replication Timing of Human Chromosome 6

  2005influential reference
• A Dynamic Switch in the Replication Timing of Key Regulator Genes in Embryonic Stem Cells upon Neural Induction

  2004cited by this paper
• Coordination of replication and transcription along a Drosophila chromosome.

  2004influential reference
• DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states.

  2004cited by this paper
• DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states.

  2004influential reference
• Control of Pancreas and Liver Gene Expression by HNF Transcription Factors

  2004cited by this paper
• Replication timing of the human genome.

  2004influential reference
• A gene atlas of the mouse and human protein-encoding transcriptomes.

  2004cited by this paper
• Synchrony in Human, Mouse and Bacterial Cell Cultures: A Comparison

  2003cited by this paper
• Heritable gene silencing in lymphocytes delays chromatid resolution without affecting the timing of DNA replication

  2003influential reference
• Replicating by the clock

  2003cited by this paper
• Identification of genes periodically expressed in the human cell cycle and their expression in tumors.

  2002cited by this paper
• Establishment of transcriptional competence in early and late S phase

  2002cited by this paper
• Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing

  2002cited by this paper
• Chromosome-wide assessment of replication timing for human chromosomes 11q and 21q: disease-related genes in timing-switch regions.

  2002cited by this paper
• Mapping of early firing origins on a replication profile of budding yeast

  2002cited by this paper
• Production of minimally disturbed synchronous cultures of hematopoietic cells.

  2002cited by this paper
• Cancer genetics: Women only

  2002cited by this paper
• Promoter-specific binding of Rap1 revealed by genome-wide maps of protein–DNA association

  2001cited by this paper
• Replication dynamics of the yeast genome.

  2001cited by this paper
• Developmental regulation of DNA replication timing at the human beta globin locus.

  2001influential reference
• Developmental regulation of DNA replication timing at the human β globin locus

  2001influential reference
• Genome-wide location and function of DNA binding proteins.

  2000cited by this paper
• Replication fork pausing and recombination or "gimme a break".

  2000cited by this paper
• Mapping replication origins

  2000cited by this paper
• Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci

  2000influential reference
• Asynchronous replication of imprinted genes is established in the gametes and maintained during development

  1999cited by this paper
• Evidence that a single replication fork proceeds from early to late replicating domains in the IgH locus in a non-B cell line.

  1999cited by this paper
• Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.

  1998cited by this paper
• Mapping of replication origins and termination sites in the Duchenne muscular dystrophy gene.

  1997cited by this paper
• Role of late replication timing in the silencing of X-linked genes.

  1996cited by this paper
• Allelic inactivation regulates olfactory receptor gene expression.

  1994cited by this paper
• High-resolution replication bands compared with morphologic G- and R-bands.

  1994cited by this paper
• When replication forks stop

  1994cited by this paper
• Allele-specific replication timing of imprinted gene regions

  1993cited by this paper
• Association of fragile X syndrome with delayed replication of the FMR1 gene.

  1993cited by this paper
• Delineation of DNA replication time zones by fluorescence in situ hybridization.

  1992influential reference
• Asynchronous replication of homologous loci on human active and inactive X chromosomes.

  1990cited by this paper
• Eukaryotic chromosome replication.

  1988cited by this paper
• Role of replication time in the control of tissue-specific gene expression.

  1987influential reference
• Role of replication time in the control of tissue-specific gene expression.

  1987cited by this paper
• Temporal order of replication of Xenopus laevis 5S ribosomal RNA genes in somatic cells.

  1986cited by this paper
• Replication timing of genes and middle repetitive sequences.

  1984cited by this paper
• Characterization of Giemsa dark- and light-band DNA.

  1982cited by this paper
• The temporal order of replication of murine immunoglobulin heavy chain constant region sequences corresponds to their linear order in the genome.

  1982cited by this paper
• Rate of DNA replication fork movement within a single mammalian cell.

  1980cited by this paper
• Eucaryotic DNA: organization of the genome for replication.

  1978cited by this paper
• Changes in the rate of DNA replication fork movement during S phase in mammalian cells.

  1975cited by this paper
• Eukaryotic chromosome replication.

  1975cited by this paper

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• Polymerase-usage sequencing identifies initiation zones with less bias across S phase in mouse embryonic stem cells

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• Emergence of replication timing during early mammalian development

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• Optimized Repli-seq: Improved DNA Replication Timing Analysis by Next-Generation Sequencing

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  2022cites this paper
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• Telomere-to-telomere human DNA replication timing profiles

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• Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency

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  2020cites this paper
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  2020cites this paper
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  2019cites this paper
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  2016cites this paper
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  2016cites this paper
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  2013cites this paper
• R/G-band boundaries: genomic instability and human disease.

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• Megabase replication domains along the human genome: relation to chromatin structure and genome organisation.

  2013cites this paper
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