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Fig. 3 | Genome Biology

Fig. 3

From: Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis

Fig. 3

The identified putative DV enhancer regions are enriched for known DV transcription factor motifs. a Known Drosophila motifs that are significantly enriched (red) or depleted (blue) at MEs or DEEs over non-differential control regions, or DEEs over MEs, are shown as sequence logos in bits on the left. The transcription factor that is known to bind the motif is shown on the right. If there are several transcription factors (TFs), all matches are shown, and the factor that is known to function during DV patterning is underlined. Significance was determined by a one-sided proportion test (* p < 0.05, ** p < 10−2, *** p < 10−3, **** p < 10−4, ***** p < 10−5 after Benjamini-Hochberg correction). b Many identified transcription factors are expressed in a DV-specific pattern themselves, e.g., localized to the mesoderm (top) or the dorsal ectoderm (bottom) in in situ hybridization images from stage 4, obtained from the Berkeley Drosophila Genome Project (BDGP) in situ hybridization database [73–75]. Among them are lov and Dll, which are expressed in the dorsal ectoderm. c Expression of lov and Dll in the dorsal ectoderm could be mediated by two enhancers identified among DEEs (lov-DEE4 and Dll-DEE-TSS). Overlapping VTs drive reporter activity similar to the endogenous genes. Both enhancers are occupied by Mad, Zen, and Zld based on ChIP-seq data, indicating direct regulation by the DV network. Dl, Twi ChIP-seq are from Tl 10b embryos, Sna ChIP-seq from wild-type embryos, and Mad, Zen, Zld ChIP-seq from gd 7 embryos. d DV regulatory network based on the rediscovered transcription factors and lov and Dll as added components (boxed). The shown regulatory interactions are based on literature knowledge, confirmed by our own ChIP-seq data. Shown in red are transcription factors that likely function as repressors, since the tissue in which they are expressed is distinct from the tissue of their target genes

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