Generating Zebrafish RNA-Less Mutant Alleles by Deleting Gene Promoters with CRISPR/Cas9

Pregnane X receptor attenuates gold nanoparticles' toxicity through accelerating zebrafish embryo hatching

It is well known that fish embryos are vulnerable to waterborne nanoparticles (NPs), with delayed hatching being the most common and sensitive endpoint. Up-regulation of hatching enzymes has been believed to be an important detoxification mechanism for NPs, but the inner mechanism for such phenomena has been seldom investigated. This study aimed to investigate the role of pregnane X receptor (Pxr) in maintaining the robustness of embryo hatching after treatment with gold nanoparticles (AuNPs, 4 and 82 nm). For this purpose, embryos from mating of 6-month-old wild-type (WT) AB strain zebrafish (Danio rerio, 3∼4-cm-length) were treated with AuNPs since 4 h post-fertilization (hpf). It was found that both AuNPs significantly inhibited embryo hatching after 52-h treatment, with Au-4 being more toxic at the same mass concentrations. At non-toxic concentrations and median effective concentrations (EC50) of delayed hatching, both AuNPs induced the mRNA expression of HEs and Pxr at 48 hpf, and Au-4 seemed to be more effective. The induction extents of HEs by AuNPs decreased when Pxr was knocked out or inhibited, indicating the role of Pxr in such process. Additionally, knockout/inhibition of Pxr significantly delayed the hatching of embryos at 56 hpf, and activation of Pxr accelerated the process at moderate concentrations. Such phenomena correlated well with the alterations in the mRNA expression and activities of HEs, indicating a fact that AuNPs activated Pxr and up-regulated HEs, which helped the detoxification of AuNPs. RNA-sequencing analysis of WT and pxr-deficient embryos at 24 hpf confirmed the alteration of he1.1&1.2. In addition, Pxr influenced mRNA encoding muscle development (muscle system process and striated muscle tissue development) and energy metabolism (carbohydrate metabolic process and ATP metabolic process), which were related to the motility of embryos and determined the hatching speed. Such function was confirmed by the reduced locomotor activity of pxr-deficient larvae at 120 hpf. Overall, these results suggested a novel role of Pxr in promoting the hatching of zebrafish embryos, which contributed to the detoxification of AuNPs.

TFAP2 paralogs facilitate chromatin access for MITF at pigmentation and cell proliferation genes

In developing melanocytes and in melanoma cells, multiple paralogs of the Activating-enhancer-binding Protein 2 family of transcription factors (TFAP2) contribute to expression of genes encoding pigmentation regulators, but their interaction with Microphthalmia transcription factor (MITF), a master regulator of these cells, is unclear. Supporting the model that TFAP2 facilitates MITF's ability to activate expression of pigmentation genes, single-cell seq analysis of zebrafish embryos revealed that pigmentation genes are only expressed in the subset of mitfa-expressing cells that also express tfap2 paralogs. To test this model in SK-MEL-28 melanoma cells we deleted the two TFAP2 paralogs with highest expression, TFAP2A and TFAP2C, creating TFAP2 knockout (TFAP2-KO) cells. We then assessed gene expression, chromatin accessibility, binding of TFAP2A and of MITF, and the chromatin marks H3K27Ac and H3K27Me3 which are characteristic of active enhancers and silenced chromatin, respectively. Integrated analyses of these datasets indicate TFAP2 paralogs directly activate enhancers near genes enriched for roles in pigmentation and proliferation, and directly repress enhancers near genes enriched for roles in cell adhesion. Consistently, compared to WT cells, TFAP2-KO cells proliferate less and adhere to one another more. TFAP2 paralogs and MITF co-operatively activate a subset of enhancers, with the former necessary for MITF binding and chromatin accessibility. By contrast, TFAP2 paralogs and MITF do not appear to co-operatively inhibit enhancers. These studies reveal a mechanism by which TFAP2 profoundly influences the set of genes activated by MITF, and thereby the phenotype of pigment cells and melanoma cells.