Using ΦC31 integrase to mediate insertion of DNA in Xenopus embryos

Instantaneous visual genotyping and facile site-specific transgenesis via CRISPR-Cas9 and phiC31 integrase

Here, we introduce 'TICIT', targeted integration by CRISPR-Cas9 and integrase technologies, which utilizes the site-specific DNA recombinase - phiC31 integrase - to insert large DNA fragments into CRISPR-Cas9 target loci. This technique, which relies on first knocking in a 39-basepair phiC31 landing site via CRISPR-Cas9, enables researchers to repeatedly perform site-specific transgenesis at the exact genomic location with high precision and efficiency. We applied this approach to devise a method for the instantaneous determination of a zebrafish's genotype simply by examining its color. When a zebrafish mutant line must be propagated as heterozygotes due to homozygous lethality, employing this method allows facile identification of a population of homozygous mutant embryos even before the mutant phenotypes manifest. Thus, it should facilitate various downstream applications, such as large-scale chemical screens. We demonstrated that TICIT could also create reporter fish driven by an endogenous promoter. Further, we identified a landing site in the tyrosinase gene that could support transgene expression in a broad spectrum of tissue and cell types. In sum, TICIT enables site-specific DNA integration without requiring complex donor DNA construction. It can yield consistent transgene expression, facilitate diverse applications in zebrafish, and may be applicable to cells in culture and other model organisms.

Global mapping of binding sites for phic31 integrase in transgenic maden-darby bovine kidney cells using ChIP-seq

Background

ΦC31 integrase, a site-specific recombinase, can efficiently target attB-bearing transgenes to endogenous pseudo attP sites within mammalian genomes. The sequence features of endogenous binding sites will help us to fully understand the site-specific recognition function by ΦC31 integrase. The present study was aimed to uncover the global map of ΦC31 integrase binding sites in bovine cells and analysis the features of these binding sites by comprehensive bioinformatics methods.

Results

In this study, we constructed a ChIP-seq method that can be used to uncover the global binding sites by phiC31 integrase. 6740 potential ΦC31 integrase binding sites were identified. A sequence motif was found that contains inverted repeats and has similarities to wild-type attP site. Using REPEATMASKER, we identified a total of 20,183 repeat-regions distributed in 50 repeat types for the 6740 binding sites. These sites enriched in “regulation of GTPase activity” of in the GO category of biological process and KEGG pathway of signal transmembrane transporter activity.

Conclusion

This study is the first time to uncover the global map of binding sites for ΦC31 integrase using ChIP-sequencing method and analysis the features of these binding sites. This method will help us to fully understand the mechanism of the site-specific integration function by phiC31 integrase and will potentially boost its genetic manipulations in both gene therapy and generation of transgenic animals.

Electronic supplementary material

The online version of this article (10.1186/s41065-018-0079-z) contains supplementary material, which is available to authorized users.

Toolbox in a tadpole: Xenopus for kidney research

Xenopus is a versatile model organism increasingly used to study organogenesis and genetic diseases. The rapid embryonic development, targeted injections, loss- and gain-of-function experiments and an increasing supply of tools for functional in vivo analysis are unique advantages of the Xenopus system. Here, we review the vast array of methods available that have facilitated its transition into a translational model. We will focus primarily on how these methods have been employed in the study of kidney development, renal function and kidney disease. Future advances in the fields of genome editing, imaging and quantitative 'omics approaches are likely to enable exciting and novel applications for Xenopus to deepen our understanding of core principles of renal development and molecular mechanisms of human kidney disease. Thus, using Xenopus in clinically relevant research diversifies the narrowing pool of "standard" model organisms and provides unique opportunities for translational research.

Transgenic Xenopus laevis for live imaging in cell and developmental biology

The stable transgenesis of genes encoding functional or spatially localized proteins, fused to fluorescent proteins such as green fluorescent protein (GFP) or red fluorescent protein (RFP), is an extremely important research tool in cell and developmental biology. Transgenic organisms constructed with fluorescent labels for cell membranes, subcellular organelles, and functional proteins have been used to investigate cell cycles, lineages, shapes, and polarity, in live animals and in cells or tissues derived from these animals. Genes of interest have been integrated and maintained in generations of transgenic animals, which have become a valuable resource for the cell and developmental biology communities. Although the use of Xenopus laevis as a transgenic model organism has been hampered by its relatively long reproduction time (compared to Drosophila melanogaster and Caenorhabditis elegans), its large embryonic cells and the ease of manipulation in early embryos have made it a historically valuable preparation that continues to have tremendous research potential. Here, we report on the Xenopus laevis transgenic lines our lab has generated and discuss their potential use in biological imaging.