Xenopus Genomics and Genetics: Progress and Prospects

Abstract

The amphibian Xenopus laevis has proved to be an outstanding model system for molecular, cell, and developmental biology, providing seminal insights on cell cycle regulation, mechanisms of translational control, and the diverse roles of intercellular signaling during vertebrate development. Over the last decade, the related species Xenopus tropicalis has arisen as a promising system for genetic analyses of vertebrate development, complementing the molecular and biochemical advantages of X. laevis. Sequencing and assembly of the X. tropicalis genome has been aided by the construction of BAC libraries and a meiotic map of simple sequence-length polymorphisms. The most recent assembly of the X. tropicalis genome includes ten “super-scaffolds” that have been assigned to the ten chromosomes. Sequencing of the X. tropicalis genome has advanced ongoing investigations of gene function, which include both traditional and PCR-based forward genetic screens, as well as morpholino-oligonucleotide-based “reverse genetic” screens. Improved methods of conventional and transposon-mediated transgenesis have also furthered functional analyses of individual genes. Moreover, newly developed genomic tools have also facilitated studies of gene regulation at transcriptional and post-transcriptional levels. Genome-wide and promoter-specific tiling arrays have been used for systems-level analyses of epigenetic regulation during early development. Analyses of noncoding RNAs expressed in oocytes and embryos have characterized piwi-protein-associated RNAs and microRNAs, and specific functions for oocyte noncoding RNAs have been identified. Regulatory functions of individual Xenopus microRNAs have been demonstrated during early axial patterning, organogenesis, and neural development. The advent of genomics resources for both Xenopus species, coupled with the ease of developmental manipulation and biochemical analysis, offers novel routes of investigation into an extensive range of regulatory processes fundamental to vertebrate cells and embryos. A description of several on-line genomics resources for Xenopus is included as an appendix.