Abstract
BackgroundDrosophila dorso-ventral (DV) patterning is one of the best-understood regulatory networks to date, and illustrates the fundamental role of enhancers in controlling patterning, cell fate specification, and morphogenesis during development. Histone acetylation such as H3K27ac is an excellent marker for active enhancers, but it is challenging to obtain precise locations for enhancers as the highest levels of this modification flank the enhancer regions. How to best identify tissue-specific enhancers in a developmental system de novo with a minimal set of data is still unclear.ResultsUsing DV patterning as a test system, we develop a simple and effective method to identify tissue-specific enhancers de novo. We sample a broad set of candidate enhancer regions using data on CREB-binding protein co-factor binding or ATAC-seq chromatin accessibility, and then identify those regions with significant differences in histone acetylation between tissues. This method identifies hundreds of novel DV enhancers and outperforms ChIP-seq data of relevant transcription factors when benchmarked with mRNA expression data and transgenic reporter assays. These DV enhancers allow the de novo discovery of the relevant transcription factor motifs involved in DV patterning and contain additional motifs that are evolutionarily conserved and for which the corresponding transcription factors are expressed in a DV-biased fashion. Finally, we identify novel target genes of the regulatory network, implicating morphogenesis genes as early targets of DV patterning.ConclusionsTaken together, our approach has expanded our knowledge of the DV patterning network even further and is a general method to identify enhancers in any developmental system, including mammalian development.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1057-2) contains supplementary material, which is available to authorized users.
Highlights
Drosophila dorso-ventral (DV) patterning is one of the best-understood regulatory networks to date, and illustrates the fundamental role of enhancers in controlling patterning, cell fate specification, and morphogenesis during development
We identify novel DV target genes, including transcription factors and signaling components, as well as genes involved in morphogenesis that may function in early tissue movements, including gastrulation
Known DV enhancers are marked by relative differences in H3K27ac across tissues To identify novel DV enhancers using H3K27ac, we focused on the most ventral and the most dorsal tissue by using Tl10b embryos and gd7 embryos
Summary
Drosophila dorso-ventral (DV) patterning is one of the best-understood regulatory networks to date, and illustrates the fundamental role of enhancers in controlling patterning, cell fate specification, and morphogenesis during development Histone acetylation such as H3K27ac is an excellent marker for active enhancers, but it is challenging to obtain precise locations for enhancers as the highest levels of this modification flank the enhancer regions. In Drosophila, DV patterning sets up the initial germ layers: mesoderm on the most ventral side, neurectoderm in the middle, and dorsal ectoderm on the dorsal side, Koenecke et al Genome Biology (2016)7:9 which gives rise to the extraembryonic amnioserosa most dorsally Patterning these tissues requires the graded activity of two conserved signal transduction pathways, the Toll (Tl) and bone morphogenetic protein (BMP) signaling pathways. Dpp activity on the dorsal side activates the transcription factor Mothers against dpp (Mad) [12]
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