(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 …
Original western blots and EMSA images.
(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 …
(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) …
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.
(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)…
(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 …
(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 …
(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 …
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 …
(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 …
(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 …
(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 …
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 …
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 |
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. …
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 |
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 …