A systems biology approach uncovers the core gene regulatory network governing iridophore fate choice from the neural crest

Abstract

Multipotent neural crest (NC) progenitors generate an astonishing array of derivatives, including neuronal, skeletal components and pigment cells (chromatophores), but the molecular mechanisms allowing balanced selection of each fate remain unknown. In zebrafish, melanocytes, iridophores and xanthophores, the three chromatophore lineages, are thought to share progenitors and so lend themselves to investigating the complex gene regulatory networks (GRNs) underlying fate segregation of NC progenitors. Although the core GRN governing melanocyte specification has been previously established, those guiding iridophore and xanthophore development remain elusive. Here we focus on the iridophore GRN, where mutant phenotypes identify the transcription factors Sox10, Tfec and Mitfa and the receptor tyrosine kinase, Ltk, as key players. Here we present expression data, as well as loss and gain of function results, guiding the derivation of an initial iridophore specification GRN. Moreover, we use an iterative process of mathematical modelling, supplemented with a Monte Carlo screening algorithm suited to the qualitative nature of the experimental data, to allow for rigorous predictive exploration of the GRN dynamics. Predictions were experimentally evaluated and testable hypotheses were derived to construct an improved version of the GRN, which we showed produced outputs consistent with experimentally observed gene expression dynamics. Our study reveals multiple important regulatory features, notably a sox10-dependent positive feedback loop between tfec and ltk driving iridophore specification; the molecular basis of sox10 maintenance throughout iridophore development; and the cooperation between sox10 and tfec in driving expression of pnp4a, a key differentiation gene. We also assess a candidate repressor of mitfa, a melanocyte-specific target of sox10. Surprisingly, our data challenge the reported role of Foxd3, an established mitfa repressor, in iridophore regulation. Our study builds upon our previous systems biology approach, by incorporating physiologically-relevant parameter values and rigorous evaluation of parameter values within a qualitative data framework, to establish for the first time the core GRN guiding specification of the iridophore lineage.

Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores

“…Melanoleucophores expressed a tyrosinase related protein 1b ( tyrp1b ) transgene that marks melanophores, whereas xantholeucophores expressed an aldehyde oxidase 5 ( aox5 ) transgene that marks xanthophores (13). Both melanoleucophores and xantholeucophores expressed a reporter for purine nucleoside phosphorylase 4a ( pnp4a ), which is expressed strongly in iridophores and at lower levels in other pigment cells (14, 15)…”

Developmental and comparative transcriptomic identification of iridophore contribution to white barring in clownfish

“…Third, we retrieved previously identified iridophore markers in the list of the most DEGs in white skin (Figure ). Among the 12 genes found in common between the clownfish white bar and zebrafish iridophores, 4 ( pnp4a , prtfdc1, tfec , and fhl2a ) were already demonstrated or inferred to be important for the development or function of iridophores in teleost fishes (Kimura et al, ; Lister et al, ; McMenamin et al, ; Petratou et al, ; Santos et al, ; Welin et al, ).…”

Blue, Black, and Stripes: Evolution and Development of Color Production and Pattern Formation in Lizards and Snakes

“…The regulation of pigment cell differentiation involves protein synthesis; transcription factor (TF) binding to cis-regulatory DNA sequences; the promotion or suppression of target gene expression, subsequent expression of TFs, signaling molecules, and cell surface receptor proteins; regulation of standing or activated signal transduction pathways; and the sequential production of pigment synthesis enzymes and other essential products for specific pigment cells. In zebrafish, the core GRNs governing melanocyte specification have been established (Greenhill et al, 2011;Pavan and Raible, 2012), and iridophore GRNs have recently been established by a systems biology approach (Higdon et al, 2013;Petratou et al, 2018). GRNs for xanthophores have not yet been fully established, but the development and patterning of pteridine synthesis and the regulation of the pteridine pathway and of its patterning are largely known in zebrafish (Ziegler, 2003).…”

“…These analyses can provide insight into gene regulatory networks (GRNs) involved in color pattern formation (Mallarino et al, 2016). However, our current understanding of the color pattern formation in vertebrates is primarily based on the studies of mouse for a simple single pigment cell type (Mills and Patterson, 2009) and zebrafish for multiple pigment cell types (e.g., Ziegler, 2003;Kelsh, 2004;Parichy, 2006;Kelsh et al, 2009;Greenhill et al, 2011;Parichy and Spiewak, 2015;Petratou et al, 2018), and little is known for the developmental mechanisms of color pattern in reptiles.…”