CLAMP and Zelda function together to promote Drosophila zygotic genome activation
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, United States
- Department of Biology, Emory University, United States
- Department of Molecular Biology, Princeton University, United States
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, United States
Figures
Figure 1 with 1 supplement
Novel pioneer factor CLAMP is essential for early embryonic development.
(A) Control maternal egfp depletion (left), maternal clamp depletion (middle), and maternal zld depletion (right) syncytial blastoderm stage embryos probed using smFISH for the pair-rule patterning …
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Figure 1—source data 1
Original western blots and EMSA images.
- https://cdn.elifesciences.org/articles/69937/elife-69937-fig1-data1-v2.zip
Figure 1—figure supplement 1
Novel pioneer factor CLAMP is essential for early embryonic development.
(A) Expression of early zygotic genes (even-skipped, runt, and neurotactin) in MTD and clamp-i embryos measured by RNA-seq (Rieder et al., 2017). Log2fold change and p-value were calculated using …
Figure 2 with 1 supplement
CLAMP regulates chromatin accessibility of a subset of the early zygotic genome.
(A) Differential accessibility (DA) analysis (left) of ATAC-seq from MTD embryos versus clamp-i embryos in 0–2 hr or 2–4 hr. Blue dots indicate non-DA sites. Pink dots indicate significant (FDR<0.1) …
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Figure 2—source data 1
ATAC-seq read counts in peak region in replicates of MTD and RNAi samples (DiffBind analysis).
Page 1. clamp-i versus MTD in 0–2 hr embryos. Page 2. clamp-i versus MTD in 2–4 hr embryos.
- https://cdn.elifesciences.org/articles/69937/elife-69937-fig2-data1-v2.xls
Figure 2—figure supplement 1
CLAMP regulates chromatin accessibility throughout ZGA.
(A) PCA plot for sample replicates in MTD and clamp-i embryos at 0–2 hr time point. (B) Pearson correlation heatmap of peaks dependent on CLAMP in MTD versus clamp-i embryos at 0–2 hr time point. (C)…
Figure 3 with 3 supplements
CLAMP and ZLD depend on each other for binding at a subset of sites.
(A) ZLD occupancy in 0–2 hr and 2–4 hr MTD and maternal clamp RNAi embryos. Data is displayed as a heatmap of z-score normalized ChIP-seq (log2 IP/input) reads in a 2-kb region centered at each …
Figure 3—figure supplement 1
CLAMP and ZLD depend on each other for chromatin binding.
(A) CLAMP occupancy in 0–2 hr and 2–4 hr MTD and maternal clamp RNAi embryos. Data is displayed as a heatmap of z-score normalized ChIP-seq (log2 IP/input) reads, in a 2-kb region centered around …
Figure 3—figure supplement 2
CLAMP and ZLD depend on each other for chromatin binding.
(A) Example IGV views of genomic loci: ChIP-seq in MTD and zld-i embryos at Hbn promoter region (upper panel) with CLAMP differential binding (down-DB) peak; Fdl (lower panel) with CLAMP non-DB peak …
Figure 3—figure supplement 3
CLAMP and ZLD depend on each other for chromatin binding.
Upper panels: Genomic distribution of ZLD lost (down-DB) or gained (up-DB) binding sites upon maternal clamp RNAi at 0–2 hr and 2–4 hr. Number of sites is noted on the plot. Lower panels: Genomic …
Figure 4
CLAMP and ZLD function together in zygotic genome activation.
(A) Percentage of CLAMP binding sites in 0–2 hr and 2–4 hr embryos distributed in maternal (n=646), early (n=69), mid- (n=73), late- (n=104), later (n=74), and silent (n=921) genes (peaks within a …
Figure 5 with 1 supplement
CLAMP and ZLD regulate gene expression via modulating chromatin accessibility.
(A) Four classes of CLAMP and ZLD co-bound peaks defined by combining ATAC-seq (this study or Hannon et al., 2017; Soluri et al., 2020) and ChIP-seq peaks in 0–2 hr MTD and RNAi embryos. Data is …
Figure 5—figure supplement 1
CLAMP-mediated chromatin accessibility is correlated with CLAMP and ZLD binding.
(A) CLAMP-related and ZLD-related peaks defined by combining ATAC-seq (this study or Hannon et al., 2017; Soluri et al., 2020) and ChIP-seq peaks in 0–2 hr MTD and RNAi embryos. Data is displayed as …
Figure 6
Model for how CLAMP and ZLD pioneer factor function together to define chromatin accessibility in early embryos.
CLAMP and ZLD function together at promoters to regulate each other’s occupancy and gene expression of genes encoding other key TFs. We defined CLAMP and ZLD co-bound peaks in early embryos, which …
Tables
Table 1
The number of total and differentially bound peaks for CLAMP and ZLD in control MTD, clamp-i, and zld-i embryos.
| ChIP-seq peaks | CLAMP | ZLD | ||||
|---|---|---|---|---|---|---|
| MTD | clamp-i | zld-i | MTD | clamp-i | zld-i | |
| 0–2 hr | 4962 | 3488 | 4746 | 6974 | 3687 | 4650 |
| 2–4 hr | 7564 | 4064 | 8279 | 8035 | 4687 | 6420 |
| Differential binding (DiffBind, DEseq2) | MTD versus zld-i | MTD versus clamp-i | ||||
| Up-DB | Down-DB | Non-DB | Up-DB | Down-DB | Non-DB | |
| 0–2 hr | 54 | 390 | 4184 | 8 | 274 | 3144 |
| 2–4 hr | 3 | 30 | 7351 | 223 | 1289 | 5672 |
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Table 1—source data 1
ChIP-seq read counts in peak regions in replicates of MTD and RNAi samples (DiffBind analysis).
Page 1. ZLD ChIP-seq in clamp-i versus MTD in 0–2 hr embryos. Page 2. ZLD ChIP-seq in clamp-i versus MTD in 2–4 hr embryos. Page 3. CLAMP ChIP-seq in zld-i versus MTD in 0–2 hr embryos. Page 4. …
- https://cdn.elifesciences.org/articles/69937/elife-69937-table1-data1-v2.xlsx
Table 2
The number of peaks in four types of CLAMP or ZLD mediated regions.
| ATAC-seq peaks (0–2 hr) | DA w/ CLAMP | DA w/o CLAMP | Non-DA w/ CLAMP | Non-DA w/o CLAMP |
|---|---|---|---|---|
| 16,597 | 74 | 203 | 1239 | 15,081 |
| ATAC-seq peaks (Hannon et al., 2017) (NC14 +12 min) | DA w/ ZLD | DA w/o ZLD | Non-DA w/ ZLD | Non-DA w/o ZLD |
| 19,146 | 976 | 2782 | 2010 | 13,378 |
| CLAMP ZLD co-bound open chromatin regions | Type I (Both DA) | Type II (CLAMP DA) | Type III (ZLD DA) | Type IV (Both non-DA) |
| 525 | 5 | 23 | 123 | 374 |
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Table 2—source data 1
Peaks locations in each CLAMP or ZLD-related category.
Page 1 Type I (n=5): both DA, CLAMP ZLD co-bound Page 2 Type II (n=23): CLAMP DA and ZLD non-DA, CLAMP ZLD co-bound Page 3 Type III (n=88): ZLD DA and CLAMP non-DA, CLAMP ZLD co-bound Page 4 Type IV …
- https://cdn.elifesciences.org/articles/69937/elife-69937-table2-data1-v2.xlsx
