Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network

Abstract

Smooth muscle plays a prominent role in many fundamental processes and diseases, yet our understanding of the transcriptional network regulating its development is very limited. The FoxF transcription factors are essential for visceral smooth muscle development in diverse species, although their direct regulatory role remains elusive. We present a transcriptional map of Biniou (a FoxF transcription factor) and Bagpipe (an Nkx factor) activity, as a first step to deciphering the developmental program regulating Drosophila visceral muscle development. A time course of chromatin immunoprecipitatation followed by microarray analysis (ChIP-on-chip) experiments and expression profiling of mutant embryos reveal a dynamic map of in vivo bound enhancers and direct target genes. While Biniou is broadly expressed, it regulates enhancers driving temporally and spatially restricted expression. In vivo reporter assays indicate that the timing of Biniou binding is a key trigger for the time span of enhancer activity. Although bagpipe and biniou mutants phenocopy each other, their regulatory potential is quite different. This network architecture was not apparent from genetic studies, and highlights Biniou as a universal regulator in all visceral muscle, regardless of its developmental origin or subsequent function. The regulatory connection of a number of Biniou target genes is conserved in mice, suggesting an ancient wiring of this developmental program.

Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes ThroughoutDrosophila melanogasterDevelopment

“…Nonetheless, downstream targets that affect these critical functions have been identified in only a subset of tissues. Studies of other transcription factors suggested that the varied processes regulated by Grh would be controlled by Grh binding to distinct regulatory regions at different stages of development (Jakobsen et al 2007;Zinzen et al 2009;Wilczynski and Furlong 2010;Spitz and Furlong 2012;Yanez-Cuna et al 2012;Slattery et al 2013Slattery et al , 2014. In contrast to this expectation, our data suggest that the Grh-binding sites remain largely unchanged over development, and that it is through occupancy of these stably bound regions that Grh regulates gene expression.…”

“…While it has been demonstrated that low-occupancy regions are less likely to contain regulatory information as compared to highoccupancy regions, there are multiple examples of low affinity binding sites driving specific gene expression (Fisher et al 2012;Ramos and Barolo 2013;Crocker et al 2015). Furthermore, binding events that are temporally dynamic over development are enriched for functional binding events, and are more predictive of activity (Jakobsen et al 2007;Li et al 2008Li et al , 2011Zinzen et al 2009;Wilczynski and Furlong 2010). Thus, there has been a focus on those DNA-binding events that change through development.…”

“…Broadly expressed transcription factors can regulate multiple, distinct developmental processes, but whether they do so through context-specific DNA-binding events, or through activities subsequent to DNA binding, remains an open question. Based on the relatively limited number of studies that have elucidated transcription factor binding over multiple stages of development, it has been suggested that functional binding events are temporally dynamic (Jakobsen et al 2007;Zinzen et al 2009;Wilczynski and Furlong 2010;Spitz and Furlong 2012;Yanez-Cuna et al 2012;Slattery et al 2013Slattery et al , 2014. These changes in binding site occupancy by sequence-specific transcription factors are regulated largely through alterations in chromatin structure that modulate the accessible regions of the genome Li et al 2011).…”

Expression of FoxC, FoxF, FoxL1, and FoxQ1 genes in the dogfish Scyliorhinus canicula defines ancient and derived roles for fox genes in vertebrate development

“…In B. floridae, FoxC is expressed in somitic mesoderm, FoxL1 in a small population of medial mesoderm adjacent to the notochord, FoxF in the ventral gut-associated mesoderm and FoxQ1 in the developing endostyle and peripharyngeal bands (Mazet et al, 2005(Mazet et al, , 2006. Some of these domains of expression, particularly FoxF in gut-associated mesoderm, may reflect more ancient roles as revealed by studies of Fox gene expression and function in Drosophila (Zaffran et al, 2001;Perez Sanchez et al, 2002;Jakobsen et al, 2007).…”

Genetic Networks Governing Heart Development

“…Its early development relies on a regulatory network of TFs homologous to the kernel factors defined in mammals, including the NKX2-5-like homeodomain factor Tinman, GATA factor Pannier, and T-box factor Dorsocross (Jin et al 2013 (Carmena et al 2002;Jakobsen et al 2007;Jin et al 2013). Genome-wide ChIP, transcriptome analysis, and computational approaches have also identified other important regulators of mesodermal lineage specification including MEF2, Biniou, and Ladybird (Sandmann et al 2006;Jakobsen et al 2007;Junion et al 2007Junion et al , 2012. Jin et al (2013) used ChIP to profile the binding sites of Tinman at two developmental stages.…”