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Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks. Nat Struct Mol Biol

Consejo Superior de Investigaciones Científicas -Universidad autónoma de Madrid, Madrid, Spain.
Nature Structural & Molecular Biology (Impact Factor: 13.31). 02/2011; 18(3):395-400. DOI: 10.1038/nsmb.1988

ABSTRACT

Genome integrity requires faithful chromosome duplication. Origins of replication, the genomic sites at which DNA replication initiates, are scattered throughout the genome. Their mapping at a genomic scale in multicellular organisms has been challenging. In this study we profiled origins in Arabidopsis thaliana by high-throughput sequencing of newly synthesized DNA and identified ~1,500 putative origins genome-wide. This was supported by chromatin immunoprecipitation and microarray (ChIP-chip) experiments to identify ORC1- and CDC6-binding sites. We validated origin activity independently by measuring the abundance of nascent DNA strands. The midpoints of most A. thaliana origin regions are preferentially located within the 5' half of genes, enriched in G+C, histone H2A.Z, H3K4me2, H3K4me3 and H4K5ac, and depleted in H3K4me1 and H3K9me2. Our data help clarify the epigenetic specification of DNA replication origins in A. thaliana and have implications for other eukaryotes.

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Available from: Roberto Solano, Apr 07, 2014
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    • "Published ChIP-seq and ChIP-chip data (Zhang et al. 2009; Costas et al. 2011; Roudier et al. 2011; Luo et al. 2012; Park et al. 2012; Stroud et al. 2012) were originally mapped to the TAIR8 version of the A. thaliana reference genome. For ChIP-seq data, 50-bp fragments were retrieved from the TAIR8 genome and mapped to TAIR10. "
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    • "The features that determine origin activation are not known although it seems clear that a local chromatin landscape, in addition to DNA sequence characteristics, are involved (Costas et al., 2011b; Sanchez et al., 2012; Mechali et al., 2013). A genome-wide map of origins (the “originome”) is now available for Arabidopsis cultured cells (Costas et al., 2011a). This dataset revealed a negative correlation between origins and CG methylation as well as a positive correlation with histone modifications frequently associated with active genes, such as H3K4me2, H3K4me3, H3ac, and H4ac, coinciding with data obtained in animal cells (Cadoret et al., 2008; Sequeira-Mendes et al., 2009; Karnani et al., 2010). "
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    • "Deposition of appropriate epigenetic marks is necessary for the expression of cell cycle-related genes, for labeling of replication origins, and, during the S-phase, for maintenance of epigenetic signatures on new DNA double helices (e.g. signatures that will regulate gene expression and establish euchromatin and heterochro- matin;Costas et al., 2011a;Dorn and Cook, 2011). SETdomain proteins represent important chromatin modifiers responsible for monomethylation, dimethylation, or trimethylation of various Lys residues on N-terminal histone tails (Kouzarides, 2007;Liu et al., 2010;Thorstensen et al., 2011). "
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