Xenomics

Abstract

Xenopus genomics, or Xenomics for short, is coming of age. Indeed, biological insight into processes such as growth factor signaling and patterning of the early embryo is now being gained by combining the value of Xenopus as a model organism for cell and developmental biology with genomic approaches. In this review I address these recent advances and explore future possibilities gained from combining this powerful experimental system with genomic approaches, as well as how our quest to understand basic biological principles will be greatly facilitated though the marriage of Xenopus and genomics.Xenopus genomics is very much in its infancy. Although largescale sequencing efforts were slow to be initiated in this system, in the past 3-4 yr there has been an explosion of genomic information accumulating in Xenopus laevis and its diploid relative, Xenopus tropicalis (Fig.1). Since the beginning of 2003, >320,000 sequences have been deposited in public repositories for X. laevis and >1,100,000 for X. tropicalis, mostly in the form of expressed sequence tags (ESTs). With this expansive amount of new sequence information, X. tropicalis recently jumped into third place on the list of organisms with the most EST's, behind human and mouse. During the same period of time, the Joint Genome Institute (JGI) has been sequencing the X. tropicalis genome, using a shotgun approach, and it has recently completed ‫ן8‬ coverage. The JGI is currently in the process of assembling the X. tropicalis genome, and it is expected that the JGI will announce its results by the end of 2005. Now that such an extensive amount of genomic information is becoming available in Xenopus, how will this be useful in our scientific pursuits? This question is best answered by further asking, "What is the ultimate value of obtaining sequence information?" If the ultimate aim is not simply to catalog genes but to understand their function, then it would be very advantageous to find the ideal organisms to study gene function. It is here where the marriage of Xenopus and genomics will reap its full benefits, as Xenopus is perhaps the best vertebrate model organism for functional genomics. Functional screensXenopus is arguably the best available vertebrate model for systematic large-scale in vivo gene function analysis. In this section I review the different types of functional screens that can be performed in Xenopus.

Cell proliferation during the early compartmentalization of the Xenopus laevis inner ear

“…Amphibians such as Xenopus offer an alternative model for unraveling mechanisms that promote regeneration in an organism that is well characterized genetically and developmentally (Nieuwkoop and Faber, 1967;Amaya, 2005). Furthermore, the increasing interest in the use of amphibians such as Xenopus to investigate cell proliferation during development of the olfactory bulb (Fritz et al, 1996), the spinal cord (Schlosser et al, 2002) and the auditory medulla (Chapman et al, 2006), will provide a foundation for comparative studies of the regenerative potential of amphibian neural and sensory tissue as compared with that of other vertebrates.…”

“…This research was motivated by the expectation that a Xenopus experimental model would offer unique opportunities for investigating the regenerative potential of inner ear epithelia in an amphibian species where there is a strong anatomical and genetic foundation for mechanistic investigations (Kay and Peng, 1991;Amaya, 2005). To this end, we used bromodeoxyuridine (BrdU) incorporation to assess cell proliferation and terminal mitosis during the initial stages of compartmentalization of the Xenopus inner ear, a period when the sacculus (an acousticovestibular organ) and the vestibular organs first begin to appear (Paterson, 1948;Nieuwkoop and Faber, 1967;Bever et al, 2003;Quick and Serrano, 2005).…”

Xenopus, an ideal model system to study vertebrate left‐right asymmetry

“…The recent advent of transgenic frog technologies in Xenopus tropicalis, which has a GRP and flow just like Xenopus laevis (Blum et al, 2009), provides further options for generating and analyzing mutant lines using all of the above-mentioned techniques. The first three examples of mutants with LR defects have already been published (Noramly et al, 2005), and more should become available as mutagenesis projects proceed (Amaya, 2005;Grammer et al, 2005; http:// tropicalis.berkeley.edu/home).…”

pTransgenesis: a cross-species, modular transgenesis resource

“…The advent of recombination-based cloning brought a series of diverse and pioneering studies showing the utility of this technology in creating DNA constructions for transgenesis (Fisher et al, 2006;Hope et al, 2004;Ikeya et al, 2005;Kappas et al, 2008;Kwan et al, 2007;Nyabi et al, 2009;Semple et al, 2010;Skarnes et al, 2011). However, none had yet been designed specifically for use in Xenopus, a widely used model organism (Amaya, 2005), and the ability to use them across multiple models was limited. When we began to develop a transgenesis plasmid resource for Xenopus, we sought to design a system that would encapsulate multiple advances demonstrated in previous Multisite Gateway-based cloning projects, but we wished to expand on them to make them more universally useful to the developmental biology community at large.…”