bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/268482

Highly efficient CRISPR/Cas9-mediated tissue specific mutagenesis in Drosophila

Poe, A. R.·Wang, B.·Sapar, M. L.·Ji, H.·Li, K.·Onabajo, T.·Fazliyeva, R.·Gibbs, M.·Qiu, Y.·Hu, Y.·Han, C.
View original source ↗Export metadata ↓

Abstract

Tissue-specific loss-of-function (LOF) analysis is an essential approach for characterizing gene function. Here we describe an efficient CRISPR-mediated tissue-restricted mutagenesis (CRISPR-TRiM) method for ablating gene function in Drosophila. This binary system consists of a tissue-specific Cas9 and a ubiquitously expressed multi-guide RNA (gRNA) transgene. To facilitate the construction of these components, we developed convenient tools for generating and evaluating enhancer-driven Cas9 lines, identified a multi-gRNA design that is highly efficient in mutagenizing somatic cells, and established an assay for testing the efficiency of multi-gRNAs in creating double-stranded breaks. We found that excision of genomic DNA induced by two gRNAs is infrequent in somatic cells, while indels more reliably cause tissue-specific LOF. Furthermore, we show that enhancer-driven Cas9 is less cytotoxic yet results in more complete gene removal than Gal4-driven Cas9 in larval neurons. Finally, we demonstrate that CRISPR-TRiM efficiently unmasks redundant gene functions in neuronal morphogenesis. Importantly, two Cas9 transgenes that turn on with different timings in the neuronal lineage revealed the extent to which gene products persist in cells after tissue-specific gene knockout. These CRISRPR tools can be applied to analyze tissue-specific gene function in many biological processes.

Explore related subjects

developmental biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Poe, A. R., Wang, B., Sapar, M. L., Ji, H., Li, K., Onabajo, T., Fazliyeva, R., Gibbs, M., Qiu, Y., Hu, Y., Han, C.. 2018-02-20. Highly efficient CRISPR/Cas9-mediated tissue specific mutagenesis in Drosophila. https://doi.org/10.1101/268482

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Coding region changes in the Hippo pathway component YAP1 contribute to body size differences among mammalian species

Animal species differ dramatically in their overall size, yet the mechanisms underlying these differences are poorly understood. The Hippo pathway, first discovered in Drosophila, and widely conserved in mammals, regulates the nuclear levels of YAP1, a transcriptional co-activator that enhances the expression of growth-promoting genes. While experimental manipulations of this pathway elicit dramatic effects on tissue growth and organ size, it is not known whether, and to what extent, evolutionary divergence of this pathway has contributed to size differences across animals. Here we show that although YAP1 protein sequence is highly conserved between diverse mammals such as humans, elephants and blue whales, it diverges considerably among rodent species. While the human YAP1 protein is very similar to that of the largest rodent, the capybara Hydrochoerus hydrochaeris, those of smaller rodents such as the mouse Mus musculus and the vole Microtus oregoni show considerable divergence. An increased ratio of non-synonymous versus synonymous substitutions (dN/dS) in clades of small rodents compared to the background is indicative of relaxed constraint in these lineages, suggesting relative positive selection. When expressed in the developing Drosophila wing, capybara YAP1 was more potent at promoting growth than that of the mouse or vole. Following transfection into mammalian cells, capybara YAP1 is more effective at promoting expression of a reporter gene than either mouse or vole YAP1. Thus, by combining computational and experimental approaches, we show that evolutionarily divergent coding-region changes in YAP1 have likely contributed to the evolution of smaller body size in clades of rodents.

developmental biology↗
bioRxiv2026

Molecular dissection of the ChAHP complex subunits Adnp and Chd4 reveals common and divergent functions in retinal development

Epigenetic remodelling is thought to regulate the progression of competence states in neural progenitor cells. Here, we examined the functions of the ChAHP chromatin remodelling complex during retinal development. ChAHP consists of the ATP-dependent nucleosome remodeller CHD4, the zinc finger and homeodomain transcription factor ADNP, and the HP1 heterochromatin proteins (Cbx1/3/5). Notably, both CHD4 and ADNP are genetically associated with neurodevelopmental disorders (NDDs), but ChAHP functions in neural development are not fully understood. In the retina, we found that both ADNP and CHD4 proteins were co-expressed ubiquitously in each cell type throughout development, and the two proteins formed a complex in vivo. Next, we generated retina-specific conditional knockouts (cKOs) to both Adnp and Chd4 using the Chx10-Cre driver. We observed phenotypic correspondence and divergence. Developmentally, we observed elevated cell death in both Adnp and Chd4 cKOs, but Adnp cKOs also exhibited deficits in progenitor numbers and proliferation. As a result, mature Adnp cKOs were hypoplastic with reductions in each cell type. We previously described a more complex phenotype in Chd4 cKOs, where cell fates were imbalanced and progenitor proliferation was prolonged, but these features were absent from the Adnp cKO. To understand how ChAHP regulates gene expression, we compared Adnp and Chd4 cKOs via scRNA-seq, which revealed common transcriptional signatures. However, Chd4 cKOs exhibited more severe effects on gene expression in line with its stronger effects on cell fate. We then performed cut&run-seq, which suggested that Adnp and Chd4 are recruited to the same genomic loci - many of which are also occupied by the Ctcf transcription factor. Taken together, our data suggest that ChAHP regulates retinal growth, but that CHD4 has additional ChAHP-independent functions in regulating progenitor fate decisions. These findings point to the idea that during neurogenesis, some brain regions may have greater dependence on ChAHP, and therefore greater vulnerability to genetic mutation.

developmental biology↗
bioRxiv2026

Fertilization offsets the maternal age effect on mouse oocytes provided the oviduct is not itself aged

Advanced maternal age compromises oocyte quality, and it is widely assumed that these deficits are transmitted to embryos. However, because most studies rely on in vivo conception, it has been difficult to separate the effects of oocyte aging from those of an aged fertilization environment. In aging mice, we observed that the fraction of ovulated oocytes forming implantation sites after in vivo conception fell ~3.7-fold, raising the question of whether this was due to reduced fertilization, reduced embryo quality or reduced support from the aged reproductive tract. Therefore we fertilized oocytes of aged and young mice in vitro with a shared young-donor sperm preparation, holding the fertilization environment constant and removing paternal variability. Hallmarks of maternal age were largely offset following fertilization in vitro: aged oocytes produced blastocysts at rates comparable to young controls, with altered - but not deficient - cell-lineage composition and no detectable impairment in development to term (E18.5) after transfer to young oviducts. Proteomic analysis revealed that, unlike the transcriptomic signature, the proteomic age signature of oocytes was not faithfully propagated to the blastocyst: for a subset of proteins, particularly those depleted in aged oocytes, the direction of the age effect reversed between oocyte and blastocyst. Comparison with parthenogenetically activated oocytes showed this divergence to be fertilization-dependent, implicating fertilization - rather than mere embryonic cleavage - as the driver of proteomic change. Stable-isotope labelling in live embryos showed that blastocysts from aged, fertilized oocytes both synthesized more new protein and retained less maternal protein than young counterparts; neither effect was detectable after parthenogenesis. Puromycin labelling, by contrast, showed a maternal-age-associated rise in bulk synthesis regardless of route. Together, these results indicate that the maternal-age effect on the oocyte proteome is labile rather than fixed and can be offset by fertilization itself, provided the maternal environment is not itself aged.

developmental biology↗