A core transcriptional network for early mesoderm development in Drosophila melanogaster

Abstract

Embryogenesis is controlled by large gene-regulatory networks, which generate spatially and temporally refined patterns of gene expression. Here, we report the characteristics of the regulatory network orchestrating early mesodermal development in the fruitfly Drosophila, where the transcription factor Twist is both necessary and sufficient to drive development. Through the integration of chromatin immunoprecipitation followed by microarray analysis (ChIP-on-chip) experiments during discrete time periods with computational approaches, we identified >2000 Twist-bound cis-regulatory modules (CRMs) and almost 500 direct target genes. Unexpectedly, Twist regulates an almost complete cassette of genes required for cell proliferation in addition to genes essential for morophogenesis and cell migration. Twist targets almost 25% of all annotated Drosophila transcription factors, which may represent the entire set of regulators necessary for the early development of this system. By combining in vivo binding data from Twist, Mef2, Tinman, and Dorsal we have constructed an initial transcriptional network of early mesoderm development. The network topology reveals extensive combinatorial binding, feed-forward regulation, and complex logical outputs as prevalent features. In addition to binary activation and repression, we suggest that Twist binds to almost all mesodermal CRMs to provide the competence to integrate inputs from more specialized transcription factors.[Keywords: Twist; Dorsal; mesoderm; ChIP-on-chip; transcriptional network; temporal regulation] Supplemental material is available at http://www.genesdev.org.

Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding

“…Context-specific binding might result from other TFs facilitating or inhibiting binding either directly or via changes to the chromatin structure and DNA accessibility (e.g., Zeitlinger et al 2003;Harbison et al 2004;Buck and Lieb 2006;Sandmann et al 2007;Heinz et al 2010;He et al 2011;John et al 2011;Kaplan et al 2011;Li et al 2011). Such a combinatorial model would be an elegant way to realize many gene regulatory states with a limited number of TFs and to achieve TF binding specificity within the context of a large genome.…”

“…However, the relation between TF motifs and in vivo binding sites is far from simple: First, there is typically a large discrepancy between the number of motif occurrences and in vivo binding sites and most of even the highestscoring motif occurrences are not bound. For example, during Drosophila embryogenesis, the mesodermal TF Twist binds to only about a thousand of the roughly 1 million Twist motifs in the genome (Sandmann et al 2007;Zeitlinger et al 2007;Zinzen et al 2009). Second, in vivo TF binding appears to be highly contextspecific, and the same TF typically binds to different genomic binding sites in different conditions (e.g., Zeitlinger et al 2003;Buck and Lieb 2006;Sandmann et al 2007;Zinzen et al 2009;Wilczynski and Furlong 2010;Palii et al 2011).…”

“…For example, during Drosophila embryogenesis, the mesodermal TF Twist binds to only about a thousand of the roughly 1 million Twist motifs in the genome (Sandmann et al 2007;Zeitlinger et al 2007;Zinzen et al 2009). Second, in vivo TF binding appears to be highly contextspecific, and the same TF typically binds to different genomic binding sites in different conditions (e.g., Zeitlinger et al 2003;Buck and Lieb 2006;Sandmann et al 2007;Zinzen et al 2009;Wilczynski and Furlong 2010;Palii et al 2011). Twist-binding sites, for example, change dynamically between different time points during embryonic mesoderm development (2-8 h post-fertilization, hpf), which cannot be attributed to changes of Twist activity (e.g., by alternative splicing or post-translational modification) or concentration (Sandmann et al 2007;Zinzen et al 2009;Wilczynski and Furlong 2010; see also Fig.…”

Evolving enhancer-promoter interactions within the tinman complex of the flour beetle,Tribolium castaneum

“…All embryos were stained for Eve expression; arrows indicate Eve expression in the dorsal and cardiac mesoderm. Previous Twist ChIP-chip assays (Sandmann et al, 2007) identified a putative enhancer downstream of the C15 transcription unit (Fig. 4A, fragment 4; Fig.…”

“…In Drosophila, mesodermal expression of lbe and lbl is regulated by two enhancers, which were identified by ChIP-chip assays for the pan-mesodermal transcription factor Twist (Sandmann et al, 2007). One of the enhancers is located within the lbl intron (Fig.…”