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Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing - Supplemental data.

Schübeler, Dirk and Scalzo, David and Kooperberg, Charles and van Steensel, Bas and Delrow, Jeffrey and Groudine, Mark (2002) Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing - Supplemental data. Nature genetics, 32 (3). pp. 438-42. ISSN 1061-4036

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Abstract

Replication of the genome before mitotic cell division is a highly regulated process that ensures the fidelity of DNA duplication. DNA replication initiates at specific locations, termed origins of replication, and progresses in a defined temporal order during the S phase of the cell cycle. The relationship between replication timing and gene expression has been the subject of some speculation. A recent genome-wide analysis in Saccharomyces cerevisiae showed no association between replication timing and gene expression. In higher eukaryotes, the limited number of genomic loci analyzed has not permitted a firm conclusion regarding this association. To explore the relationship between DNA replication and gene expression in higher eukaryotes, we developed a strategy to measure the timing of DNA replication for thousands of genes in a single DNA array hybridization experiment. Using this approach, we generated a genome-wide map of replication timing for Drosophila melanogaster. Moreover, by surveying over 40% of all D. melanogaster genes, we found a strong correlation between DNA replication early in S phase and transcriptional activity. As this correlation does not exist in S. cerevisiae, this interplay between DNA replication and transcription may be a unique characteristic of higher eukaryotes.

Item Type: Article
Additional Information: The files contain the ID of each listed gene according to reference 6 of the manuscript (Rubin, G.M. et al. A Drosophila complementary DNA resource. Science 287, 2222-2224 (2000)). These ID’s can be searched via flybase (http://flybase.bio.indiana.edu/). The replication timing ratio (early over late) is provided in log2 scale for the raw and smoothed values (see Figure 2a of the manuscript for illustration). In addition the expression status of each gene is given (1=expressed, 0=not expressed, 8=undefined). In the event you encounter difficulties, have further questions or would like to obtain additional data sets please contact Dirk Schübeler (dschubel@fhcrc.org) or Mark Groudine (markg@fhcrc.org).
DOI: 10.1038/ng1005
PubMed ID: 12355067
Keywords or MeSH Headings: Animals; Bromodeoxyuridine/pharmacology; Cell Cycle; Cell Separation; DNA Replication; DNA, Complementary/metabolism; Drosophila melanogaster/genetics; Flow Cytometry; Genome; Nucleic Acid Hybridization; Oligonucleotide Array Sequence Analysis; Polymerase Chain Reaction; Precipitin Tests; S Phase; Time Factors; Transcription, Genetic;
Depositing User: Library Staff
Date Deposited: 18 Oct 2011 18:56
Last Modified: 14 Feb 2012 14:44
URI: http://authors.fhcrc.org/id/eprint/505

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