The Hitchhiker's guide to Xenopus genetics

Abstract

Summary A decade after the human genome sequence, most vertebrate gene functions remain poorly understood, limiting benefits to human health from rapidly advancing genomic technologies. Systematic in vivo functional analysis is ideally suited to the experimentally accessible Xenopus embryo, which combines embryological accessibility with a broad range of transgenic, biochemical and gain-of-function assays. The diploid X. tropicalis adds loss-of-function genetics and enhanced genomics to this repertoire. In the last decade diverse phenotypes have been recovered from genetic screens, mutations have been cloned, and reverse genetics in the form of TILLING and targeted gene editing have been established. Simple haploid genetics and gynogenesis and the very large number of embryos produced streamline screening and mapping. Improved genomic resources and the revolution in high-throughput sequencing are transforming mutation cloning and reverse genetic approaches. The combination of loss-of-function mutant backgrounds with the diverse array of conventional Xenopus assays offers a uniquely flexible platform for analysis of gene function in vertebrate development.

Understanding the evolution and development of neurosensory transcription factors of the ear to enhance therapeutic translation

“…If we take the approach that the main problem we need to understand is the topologically restricted upregulation of a few TFs that induce hair cells directly through transdifferentiation (Yoo et al 2011), or allow transfection with Atoh1 to effectively differentiate new hair cells, or allow hair cells generated in vitro to differentiate appropriately, we can then begin to work on genetically engineered mouse models that allow us to test certain premises. Alternatively, we can use the molecular knowledge at hand and try, for example, to transform the basilar papilla of frogs (Fritzsch and Wake 1988) into a mammalian type of organ using modern genetic techniques now possible in these animals (Abu-Daya et al 2012), thus demonstrating that we indeed understand all the relevant genes.…”

Efficient high-throughput sequencing of a laser microdissected chromosome arm

“…This model system is particularly valuable for studies of early vertebrate embryonic development [3,4], functional genomics [5,6], cell biology [3,7], and vertebrate genome evolution [8]. Its 1.7 × 10 9 bp genome was sequenced [9] and a genetic map covering its 10 chromosomes was constructed [10].…”

Subfunctionalization of Paralogous Aryl Hydrocarbon Receptors from the FrogXenopus Laevis: Distinct Target Genes and Differential Responses to Specific Agonists in a Single Cell Type

“…TCDD is an agonist for both receptors, although it exhibits 20-to 50-fold lower affinity than for mouse AHR, and corresponding low potency in DNA mobility shift assays and transactivation assays (Lavine et al, 2005). Conventional wisdom holds that X. laevis alloalleles typically have redundant functions, since emergence of developmental phenotypes often requires morpholino knockdown of both genes (Abu-Daya et al, 2012). However, some gene duplicates show evidence of functional divergence (Chain and Evans, 2006;Hellsten et al, 2007).…”