Growth factor signalling & functional genomics in Xenopus and zebrafish.
University of California, Irvine
School of Biological Sciences
Developmental and Cell Biology
University of California, Irvine
Gene Regulatory Networks Regulating Endoderm Development A major unanswered question in biology is how differentiation of the myriad cell types of the adult body is hardwired in the genome. Using the frog as a model system, our goal is to elucidate the mechanisms controlling endoderm formation by combining experimental (e.g., ChIPseq and RNAseq) and computational approaches. Production of a thorough endodermal gene regulatory network in frog will provide a useful framework for prediction, that is applicable to early mouse and human embryogenesis, thereby offering valuable knowledge to the broader scientific community for reprogramming stem cells along endodermal cell lineages. Gene regulatory Network – Emergence of the primary germ layers is among the earliest events of cell specification in animal development. Understanding the mechanisms of germ layer formation and subsequent patterning has implications for the treatment of human disease. Our goal is to describe the underlying logic of genetic programs regulating vertebrate mesendoderm development. Traditionally, Gene Regulatory Network (GRN)s have been constructed using a combination of mapping of transcription factor (TF) binding sites, physical binding of TFs to these sites, and demonstration of the importance of both to gene expression output. This approach is both labor and time intensive. Another approach, utilizing a combination of computational methods with extensive perturbation analysis, can produce a GRN that, while lacking in the details of direct physical interactions, has the advantage of rapidly generating a global perspective. We generated large transcriptome profiles from tightly spaced stages of early Xenopus embryogenesis to permit modeling of the dynamics of changes in transcript levels. These data are incorporated along with morpholino knockdown studies to perturb relevant gene expression. Computational modeling has been used to identify critical core networks regulating endodermal development.
BMP Signaling in Preimplantation Mammalian Development: Using quantitative imaging techniques and analyses, we map and quantitate the dynamic activities of BMP signaling activities in preimplantation mouse embryos and demonstrate for the first time the biological function and mechanism of BMP signaling in the preimplantation mammalian embryos. We show that BMP signaling regulates cell division and is critical for the establishment of mouse blastocysts.Our work will shed light on an issue of early pregnancy loss: failure of the blastocyst to undergo normal development. Genome engineering using the CRISPR/Cas9: The CRISPR/Cas9 system relies upon the formation of double-stranded hybrids between synthetic guide RNA and genomic DNA and confers mutations in the genome. With Xenopus, the ability to microinject hundreds of synchronous, in vitro-fertilized embryos represents a significant advantage over other systems for examining mutations in the F0 generation. We use Xenopus tropicalis and develop methods to eliminate a large genomic region and induce a homologous recombination at a desired locus within the genome.