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. 2011;12(5):R43.
doi: 10.1186/gb-2011-12-5-r43. Epub 2011 May 11.

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

Sean Thomas  1 , Xiao-Yong Li, Peter J Sabo, Richard Sandstrom, Robert E Thurman, Theresa K Canfield, Erika Giste, William Fisher, Ann Hammonds, Susan E Celniker, Mark D Biggin, John A Stamatoyannopoulos
Affiliations

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

Sean Thomas et al. Genome Biol. 2011.

Abstract

Background: The 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.

Results: We 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.

Conclusions: Our 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.

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Figures

Figure 1
Figure 1
DHSs exhibit programmed developmental changes (a,b). Developmental profiling at ftz and brk loci. The density of mapped DNaseI cleavages (150-bp sliding window, step 20 bp) is shown for stages 5 (green), 9 (orange), 10 (red), 11 (blue) and 14 (purple) across a 50-kb region of the D. melanogaster genome that includes the (a) ftz and (b) brk genes. Locations of known cis-regulatory modules (CRMs) are indicated with red bars and underlying shaded regions. CRMs shown are all known to be active at stage 5 and inactive at later stages except the one indicated with an asterisk, which is a neuronal CRM active after stage 5. Temporally dynamic patterning of chromatin accessibility at DHSs is evident in up- and down-regulation of accessibility during embryo development. (c) High reproducibility of DNaseI sensitivity profiles. The pairwise Pearson correlations between DNase I cleavage density datasets from different stages (or between replicates of the same stage, along the diagonal) are indicated in a spectrum from red (extremely high correlation) to white (moderate correlation). The largest differences are observed between stage 14 and earlier stages. (d) Developmental propogation of DHSs. Stage 9 DHSs were divided into two groups, those observed at stage 5 and those that arise during the transition from stages 5 to 9. Likewise for stages 10, 11, and 14 the percentages of DHSs are depicted according to stage of temporal origin: stage 5 (green), 9 (orange), 10 (red), 11 (blue) and 14 (purple). The majority of sites (approximately 55%) observed at stage 5 are carried forward through stage 14.
Figure 2
Figure 2
DHSs overlap orthogonally-measured functional regulatory elements. (a) DHS locations correlate with functional regulatory sites from orthogonal datasets. Pie chart depicting the percentage of all DHSs identified across all stages in non-coding sequence (n = 35,769 at FDR 1%) that overlap the binding locations of other factors: CTCF, ORC, and/or any 1 of 21 developmental transcription factors. (b) DHSs are enriched at transcription start sites (TSSs) relative to genomic feature percentage. The bar graph depicts the percentage of all 1% FDR DHSs identified across all stages whose central nucleotides are located within 100 bp of a TSS, or in 5' UTRs, coding sequences, introns, 3' UTRs or between genes (intergenic). (c) Core promoter composition directs temporal changes in accessibility of TSSs. The peak in DNase I cleavage density was determined for each stage at the -60 to +40 regions of each promoter, and was clustered using kmeans. The average peak density at each stage and for each cluster is shown at left in a spectrum from yellow (high) to blue (low), forming two metaclusters: one that is constitutively high or exhibits a decrease in accessibility during development (top panels), and another set of promoters that exhibit increasing accessibility during development (bottom panels). For each cluster, the relative enrichments of each of six previously identified core promoter motifs found in each cluster are shown in a spectrum from red (high) to white (low), with the sequence logos for each motif presented on the right. Three motifs, the DNA replication-related element (DREF), r1 and r7, were greatly enriched within constitutive/down-regulated promoters, while the downstream promoter element (DPE), the initiator (INR), and MTE (motif ten element) were enriched in the upregulated promoters. (d) Different promoter classes exhibit distinct structural morphologies. Chromatin accessibility in terms of mean DNaseI tag density was plotted within a 1-kb window of the TSS for clusters indicated as (i) and (ii) in panel (c). Chromatin accessibility for stage 5 is shown in green and that for stage 14 in purple. In addition to the developmental profiling of these promoters, (i) shows a distinct double-peaked pattern that is different from the patterns of DNaseI cleavage around other promoter types.
Figure 3
Figure 3
Chromatin domains of embryonic cells in vivo show extensive differences from those in cell cultures. (a) The number of DHSs per megabase is plotted for DHSs from stage 5 embryos (white), stage 14 embryos (gray) and Kc cells for DHSs mapping to each of the five chromatin states annotated in Kc cells (red, yellow, green, blue, and black). A much larger proportion of DHSs in Kc cells map to active chromatin than to repressive chromatin, while DHSs from stage 5 and 14 are divided among the Kc domains. (b) The log ratio of embryo to Kc DHSs/Mb shown in panel (a), showing the enrichment of embryonic DHSs at regions that represent repressed chromatin in Kc cells. These enrichments suggest extensive plasticity between the two Drosophila systems. (c) An example of chromatin that is active in Kc cells but not in embryos. Plotted for stage 5 embryos and Kc cells is the DNaseI density and colored chromatin state (red and yellow = active, blue and black = repressive). (d) An example of chromatin that is active in embryos but not in Kc cells.
Figure 4
Figure 4
Chromatin accessibility patterns at developmentally dynamic elements. Developmentally dynamic elements (DDEs; see text for definition) were clustered according to quantitative accessibility patterns, and ordered according to the time of peak accessibility. (a) Number of DDEs in each cluster. (b) Average accessibility at each stage for all regions within the cluster. Each row in panels (a) and (b) represents a distinct cluster (n = 65). (c) Selected clusters from (b), which are expanded to the resolution of individual elements, wherein each pixel row depicts DNaseI sensitivity (raw tag density, highest in yellow) in a 10-kb window around each DDE in the cluster.
Figure 5
Figure 5
Developmentally dynamic domains are enriched in regulatory genes. (a) Density of DDEs plotted across chromosome 2R. Peaks in DDE density above a statistical background (dotted grey line) were labeled by associated gene name and colored by gene ontology (GO) category. (b) The median phastcons conservation score (and 95% confidence intervals) for all DDEs that map to non-coding locations is shown alongside the median and intervals calculated for randomly chosen non-coding sites within the genome. (c) DNaseI tag density across an approximately 30-kb region of chromosome 2R around ppa, indicated with an asterisk in (a,c), illustrating an exemplary developmentally dynamic domain composed of clustered DDEs (red arrows).
Figure 6
Figure 6
DNaseI patterns correlate with in situ spatio-temporal expression patterns and demonstrate the high sensitivity of the assay. For each panel, DNAse I tag densities for four genes at stages 5, 9, 10, 11 and 14 are shown in green, orange, red, blue, and purple, respectively. On the left of the accessibility plots for each stage are images from the BDGP in situ mRNA expression database of that gene during the relevant stage. (a,b) Decreases in chromatin accessibility near the pxb (a) and CG10479 (b) genes were associated with concomitant changes in spatio-temporal expression of the genes in vivo. (c,d) Increases in chromatin accessibility through development at the CG9747 (c) and CG9331 (d) genes were associated with increases in expression of the gene in vivo. Even though a relatively low percentage of cells are expressing the CG9747 gene at the latest stage in (c), an associated change in chromatin accessibility is still reflected in the chromatin accessibility profile, demonstrating the sensitivity of the DNaseI assay.
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References

    1. Graf T, Enver T. Forcing cells to change lineages. Nature. 2009;462:587–594. doi: 10.1038/nature08533. - DOI - PubMed
    1. Campos-Ortega JA, aH V. The Embryonic Development of Drosophila melanogaster. Second. Berlin: Springer-Verlag; 1997.
    1. Weigmann K, Klapper R, Strasser T, Rickert C, Technau G, Jackle H, Janning W, Klambt C. FlyMove--a new way to look at development of Drosophila. Trends Genet. 2003;19:310–311. doi: 10.1016/S0168-9525(03)00050-7. - DOI - PubMed
    1. Lewis EB. A gene complex controlling segmentation in Drosophila. Nature. 1978;276:565–570. doi: 10.1038/276565a0. - DOI - PubMed
    1. Nusslein-Volhard C, Wieschaus E. Mutations affecting segment number and polarity in Drosophila. Nature. 1980;287:795–801. doi: 10.1038/287795a0. - DOI - PubMed

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