Novel gene regulatory networks underlying two specialized modes of craniofacial development in a new model system of pupfishes

Project Summary The study of the genetic basis of craniofacial adaptations in naturally divergent groups of species can provide an opportunity to uncover novel gene networks and genome regulatory elements with clinical relevance. One of the most remarkable examples of craniofacial diversification across vertebrates is represented in teleost fishes, often associated with their diverse and highly specialized modes of feeding. In my early postdoctoral career, I leveraged a recently established evolutionary model of Cyprinodon pupfishes and established it as a new model system in eco-evo-devo1. This radiation is endemic to San Salvador Island (SSI), and includes a generalist pupfish (Cyprinodon variegatus), and two trophic specialists, the scale-eater C. desquamator, with longer oral jaws, increased oral tooth number, and larger mandibular muscles and the molluscivore, C. brontotheroides, with a shorter jaw with and a novel maxillary extension. Only a few mutations are found to be fixed between specialists2, with almost all of them found in regulatory or intronic regions, suggesting that the genetic changes underlying SSI pupfish craniofacial divergence lie in regions of the genome that affect gene expression control. I hypothesize that temporal and spatial changes in the expression of novel craniofacial candidate genes within the specialist’s gene regulatory networks (i.e., gba3, pycr3, or galr2a) are caused by dynamics differences in the chromatin state of their regulatory regions during development, which in turns, underpins the divergent craniofacial morphological development observed in SSI pupfishes. To test this, I will combine tissue-specific differential expression analysis (Aim 1) with genome-wide studies of chromatin accessibility (Aim 2) in three developmental stages (embryonic pharyngula, hatched larvae, and metamorphic fry) from divergent and non-divergent tissues among SSI pupfish species (oral jaws vs. tail caudal region). In Aim 1, I will identify tissue-specific and specialist-specific spatiotemporal gene regulatory networks (GRNs) by analyzing tissue-specific differential gene expression (DGE) (Aim 1.1) and alternative splicing identification (Aim 1.2) between SSI pupfish’s transcriptomes, life stages, and tissues. In Aim 2, I will explore chromatin state dynamics by analyzing tissue-specific chromatin accessibility (ATAC-seq) across SSI species, life stages, and tissues. I will integrate the spatiotemporal dynamics of DGE and alternative splice variants with chromatin accessibility analyses to build a predictive model to identify and test novel craniofacial gene networks and regulatory regions crucial for pupfish craniofacial divergence (Aim 3.1). The top 5 novel craniofacial candidate genes within the inferred GRN and with paired differences in chromatin accessibility will be tested using HCR (Aim 3.1), CRISPR-Cas9 gene editing (Aim 3.2), and Tol2 transgenesis (Aim 3.3). This study will reveal the different levels of genome regulation governing the evolution and development of craniofacial divergence, opening new avenues of research to understand the genomic basis of craniofacial specialization with potential implications for human craniofacial variation and disease.