Abstract
Functional characterisation of proteins and large-scale, systems-level studies are enabled by extensive sets of cloned open reading frames (ORFs) in an easily-accessible format that enables many different applications. Here we report the release of the first stage of the Xenopus ORFeome, which contains 8673 ORFs from the Xenopus Gene Collection (XGC) for Xenopus laevis, cloned into a Gateway® donor vector enabling rapid in-frame transfer of the ORFs to expression vectors. This resource represents an estimated 7871 unique genes, approximately 40% of the non-redundant X. laevis gene complement, and includes 2724 genes where the human ortholog has an association with disease. Transfer into the Gateway system was validated by 5′ and 3′ end sequencing of the entire collection and protein expression of a set of test clones. In a parallel process, the underlying ORF predictions from the original XGC collection were re-analysed to verify quality and full-length status, identifying those proteins likely to exhibit truncations when translated. These data are integrated into Xenbase, the Xenopus community database, which associates genomic, expression, function and human disease model metadata to each ORF, enabling end-users to search for ORFeome clones with links to commercial distributors of the collection. When coupled with the experimental advantages of Xenopus eggs and embryos, the ORFeome collection represents a valuable resource for functional genomics and disease modelling.
Highlights
Xenopus is a powerful vertebrate model system for investigating protein function and it has a rich history of functional genomics (Harland and Grainger, 2011)
In this context it may be important to bear in mind that some X. laevis proteins found in public repositories are likely to have been defined from the Xenopus Gene Collection (XGC) reference sequence, and we suggest that this data on its own may be insufficient to establish the veracity of the published open reading frames (ORFs)
To facilitate the use of the Xenopus ORFeome resource in experiments aimed at modelling human disease in Xenopus, we have identified those genes in the collection whose human orthologs are, either directly or indirectly, implicated in disease; these may prove useful starting points for functional investigation
Summary
Xenopus is a powerful vertebrate model system for investigating protein function and it has a rich history of functional genomics (Harland and Grainger, 2011). There are currently two members of the genus used for biomedical research: the earlier adopted, allotetraploid Xenopus laevis, and its slightly smaller cousin Xenopus tropicalis, which has a normal diploid DNA complement. Both species are widely used, and share the key characteristic of large, abundant, externally developing eggs and embryos, making them ideally suited for the discovery and analysis of protein function. Many well-known developmental regulators such as Noggin (Smith and Harland, 1992) and Dickkopf (Glinka et al, 1998) were first identified by functional screening of synthetic mRNA from cDNA libraries injected into Xenopus n Corresponding author.
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