Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis
- Howard Hughes Medical Institute, Princeton University, United States
Figures
Figure 1 with 26 supplements
Sequential establishment of chromatin accessibility at the MBT.
(A) (Left column) Single embryos were collected for ATAC seq at the indicated time points. Micrographs show stage-matched panels from a time-lapse image of a single Histone H2Av-GFP embryo. Scale …
Figure 1—figure supplement 1
Selection of metaphase-staged embryos and inter-replicate reproducibility.
(A) Probability of selecting embryos at interphase stages based on time following observation of the prior anaphase (see Materials and methods). Time-lapse movies of wild-type embryos (n = 23) were …
Figure 1—figure supplement 2
Fraction of accessible peaks during metaphase.
(A) Peaks were called on pooled biological replicates corresponding to metaphase stages, and the fraction of peaks overlapping with accessible peaks during interphase stages was calculated. (B) The …
Figure 1—figure supplement 3
Read-length distribution and comparison of interphase and metaphase library preparations.
Uniquely-mapping duplicate-filtered paired-end sequencing read sets were pooled by timepoint. A random sample of 100,000 reads for each timepoint was selected and the distribution of read lengths …
Figure 1—figure supplement 4
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Figure 2 with 2 supplements
Dynamic acquisition of chromatin accessibility is regulated by the N:C ratio.
(A) Cell cycle times for diploid (+/+, n = 21) and haploid embryos (ssm, n = 12) were measured by time lapse confocal imaging of His2Av-GFP. Mean cell cycle times ± SEM are indicated. Colored …
Figure 2—figure supplement 1
Examples of N:C-ratio-dependent regions.
Each plot shows the accessibility profiles over time for diploid (left, blue, NC11 to NC13) and haploid (right, green, NC12 to NC14) samples at four regions selected on the basis of the distribution …
Figure 2—figure supplement 2
Examples of regions that gain accessibility independently of the N:C ratio.
Each plot shows the accessibility profiles over time for diploid (left, blue, NC11 to NC13) and haploid (right, green, NC12 to NC14) samples at four regions selected on the basis of the distribution …
Figure 3 with 1 supplement
Patterns of stable and dynamic chromatin accessibility over the cell cycle.
(A) Genome-wide mean ATAC-open coverage is plotted (red, error bars show std. dev. between peaks, n = 9824) over the mean scaled heterogeneity in PCNA-EGFP to estimate DNA replication activity …
Figure 3—figure supplement 1
Example of PCNA-EGFP imaging and analysis.
Top panels show representative frames from one time-lapse image of a PCNA-EGFP embryo at the indicated timepoints during NC13. Note the distribution of brighter foci over time. Scale bar = 10 μm. An …
Figure 4 with 2 supplements
Attenuation of replication coupled nucleosome disruption at the MBT.
(A) Predicted nucleosome occupancy is plotted for the selected time points (top) for the 800 bp region flanking a set of early embryonic promoters, centered over the TSS. These timepoints correspond …
Figure 4—figure supplement 1
Nucleosome positioning over promoters.
(A) Predicted nucleosome occupancy is plotted for all time points (top) for the 800 bp region flanking a set of early embryonic promoters, centered over the TSS. Promoters are ordered on the y-axis …
Figure 4—figure supplement 2
Changes in accessibility at nucleosome-free regions over the cell cycle.
To calculate changes in chromatin accessibility at NFRs over the cell cycle, the maximum extent of each NFR was calculated from the predicted extreme positions of −1 and +1 nucleosomes as determined …
Additional files
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Supplementary file 1
Sample summary.
- https://doi.org/10.7554/eLife.20148.037
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Supplementary file 2
Sample metadata.
- https://doi.org/10.7554/eLife.20148.038
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Supplementary file 3
Annotated peak regions used in the analysis.
- https://doi.org/10.7554/eLife.20148.039
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Supplementary file 4
Annotated promoter regions.
- https://doi.org/10.7554/eLife.20148.040
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Supplementary file 5
Code example for data normalization in R markdown (.rmd) format.
- https://doi.org/10.7554/eLife.20148.041
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Supplementary file 6
Code example for data normalization in. pdf format.
- https://doi.org/10.7554/eLife.20148.042
