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


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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    ABSTRACT: The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intra-chromosome interaction rates than neighboring regions, representing a dominant local structural feature of genome conformation in A. thaliana. These regions, which appear as positive strips on two-dimensional representations of chromatin interaction, are enriched in epigenetic marks H3K27me3, H3.1 and H3.3. We also identify over 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not an obvious feature of A. thaliana genome packing, we found over 1,000 regions that have properties of TAD boundaries, and a similar number of regions analogous to the interior of TADs. The insulator-like, TAD-boundary-like, and TAD-interior-like regions are each enriched for distinct epigenetic marks, and are each correlated with different gene expression levels. We conclude that epigenetic modifications, gene density, and transcriptional activity combine to shape the local packing of the A. thaliana nuclear genome.
    Genome Research 11/2014; DOI:10.1101/gr.170332.113 · 14.63 Impact Factor
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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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    ABSTRACT: The cell cycle is defined by a series of complex events, finely coordinated through hormonal, developmental and environmental signals, which occur in a unidirectional manner and end up in producing two daughter cells. Accumulating evidence reveals that chromatin is not a static entity throughout the cell cycle. In fact, there are many changes that include nucleosome remodeling, histone modifications, deposition and exchange, among others. Interestingly, it is possible to correlate the occurrence of several of these chromatin-related events with specific processes necessary for cell cycle progression, e.g., licensing of DNA replication origins, the E2F-dependent transcriptional wave in G1, the activation of replication origins in S-phase, the G2-specific transcription of genes required for mitosis or the chromatin packaging occurring in mitosis. Therefore, an emerging view is that chromatin dynamics must be considered as an intrinsic part of cell cycle regulation. In this article, we review the main features of several key chromatin events that occur at defined times throughout the cell cycle and discuss whether they are actually controlling the transit through specific cell cycle stages.
    Frontiers in Plant Science 07/2014; 5:369. DOI:10.3389/fpls.2014.00369 · 3.95 Impact Factor
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    • "Furthermore, they are a useful resource to identify potentially relevant structural and functional elements, or combinations of them, in the Arabidopsis genome. RESULTS AND DISCUSSION High-Resolution Identification of Chromatin States Our computational procedure started from the published profiles of nine histone modification marks (H3K9me2, H3K27me1, H4K5ac, H3K4me1, H2Bub, H3K36me3, H3K4me2, H3K4me3, and H3K27me3), three histone variants (H2A.Z, H3.1, and H3.3), the nucleosome density (total H3 histone content), the genomic G+C content, and CG methylated residues (Supplemental Data Set 1) (Bernatavichute et al., 2008; Zilberman et al., 2008; Zhang et al., 2009; Costas et al., 2011; Roudier et al., 2011; Stroud et al., 2012). In addition, we generated genome-wide chromatin immunoprecipitation (ChIP)-chip data for H3K9ac and H3K14ac. "
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    ABSTRACT: Chromatin is of major relevance for gene expression, cell division, and differentiation. Here, we determined the landscape of Arabidopsis thaliana chromatin states using 16 features, including DNA sequence, CG methylation, histone variants, and modifications. The combinatorial complexity of chromatin can be reduced to nine states that describe chromatin with high resolution and robustness. Each chromatin state has a strong propensity to associate with a subset of other states defining a discrete number of chromatin motifs. These topographical relationships revealed that an intergenic state, characterized by H3K27me3 and slightly enriched in activation marks, physically separates the canonical Polycomb chromatin and two heterochromatin states from the rest of the euchromatin domains. Genomic elements are distinguished by specific chromatin states: four states span genes from transcriptional start sites (TSS) to termination sites and two contain regulatory regions upstream of TSS. Polycomb regions and the rest of the euchromatin can be connected by two major chromatin paths. Sequential chromatin immunoprecipitation experiments demonstrated the occurrence of H3K27me3 and H3K4me3 in the same chromatin fiber, within a two to three nucleosome size range. Our data provide insight into the Arabidopsis genome topography and the establishment of gene expression patterns, specification of DNA replication origins, and definition of chromatin domains.
    The Plant Cell 06/2014; 26(6). DOI:10.1105/tpc.114.124578 · 9.34 Impact Factor
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