Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

By Sean Thomas, Xiaoyong Li, P. Sabo, R. Sandstrom, Robert E. Thurman, T. Canfield, Erika Giste, W. Fisher, Ann Hammonds, S. Celniker and 2 more. 2011

191 citations recorded by the source corpus.

BackgroundThe development of complex organisms is believed to involve progressive restrictions in cellular fate. Understanding the scope and features of chromatin dynamics during embryogenesis, and identifying regulatory elements important for directing developmental processes remain key goals of developmental biology.ResultsWe used in vivo DNaseI sensitivity to map the locations of regulatory elements, and explore the changing chromatin landscape during the first 11 hours of Drosophila embryonic development. We identified thousands of conserved, developmentally dynamic, distal DNaseI hypersensitive sites associated with spatial and temporal expression patterning of linked genes and with large regions of chromatin plasticity. We observed a nearly uniform balance between developmentally up- and down-regulated DNaseI hypersensitive sites. Analysis of promoter chromatin architecture revealed a novel role for classical core promoter sequence elements in directing temporally regulated chromatin remodeling. Another unexpected feature of the chromatin landscape was the presence of localized accessibility over many protein-coding regions, subsets of which were developmentally regulated or associated with the transcription of genes with prominent maternal RNA contributions in the blastoderm.ConclusionsOur results provide a global view of the rich and dynamic chromatin landscape of early animal development, as well as novel insights into the organization of developmentally regulated chromatin features.

Subfields: Molecular Biology

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Citations in the corpus

Iterative random forests to discover predictive and stable high-order interactions (2017, methodology): “For instance, databases generated by the Berkeley Drosophila Transcriptional Network Project (BDTNP) and ENCODE consortium provide maps of transcription factor (TF) binding events and chromatin marks for substantial fractions of the regulatory factors active in the model organism Drosophila melanoga”
Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo (2015, background): “species (Lee et al. 2007; Schones et al. 2008; Weiner et al. 2010; Thomas et al. 2011; Valouev et al. 2011).”
Genome-scale functional characterization of Drosophila developmental enhancers in vivo (2014, background): “Takentogetherthisworkcomplementseffortsthatstudychromatin properties 2,19,20 orcharacterizeenhancersatdefinedstagesandinselected tissues 5–7, 15, 16 .”
Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in Drosophila (2014, background): “In Drosophila, there is a strong correlation between chromatin accessibility and the overlapping patterns of TF binding (Kaplan et al. 2011; Li et al. 2011; Thomas et al. 2011; Bonn et al. 2012), but future experiments will be required to unravel the mechanisms that control chromatin accessibility.”
Sequence and chromatin determinants of cell-type–specific transcription factor binding (2012, background): “These include histone modifications (Barrera et al. 2008; Heintzman et al. 2009), DNA methylation status (Deaton et al. 2011; Wiench et al. 2011), and accessibility of regulatory elements as measured by DNase sensitivity (Boyle et al. 2011; Thomas et al. 2011).”
Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition (2014, background): “Enhancers are ordered by chromatin accessibility, as measured by DNaseI–seq signals from cycle 14 embryos (Thomas et al., 2011) from high (top) to low (bottom).”
Zelda potentiates morphogen activity by increasing chromatin accessibility (2014, unknown): “ously [41], with some modifications.”
Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition (2011, methodology): “(A) Histogram of DNA accessibility based on DNaseI hypersensitivity from [20] among the most strongly bound 1,000 ZLD peaks at cycle 8 (red) and among randomly shuffled peak positions (blue).”