Epigenetic profiling of the developing zebrafish embryo, and technical developments towards cloning zebrafish and isolating pluripotent stem cells

Abstract

In normal embryonic development, cells generated from a fertilised oocyte lose their pluripotent status and become restricted to a particular differentiation pathway. This production of functionally distinct cell lineages is thought to be mediated by epigenetic processes that help control gene expression both temporally and spatially without any changes to the DNA sequence. These epigenetic changes consist of posttranslational modifications of the N-terminal tails of histones and differential DNA methylation. Together these act by altering local chromatin structure, which in turn directs gene transcription by regulating the accessibility of the underlying DNA. To examine the potential developmental roles of these modifications, we determined the global cellular patterns of DNA methylation, as well as histone H3 lysine 9 (H3K9) and histone H4 lysine 20 (H4K20) methylation in the developing zebrafish embryo. These modifications are seen as hallmarks of heterochromatin, which consists of DNA that is tightly packaged, gene-poor and transcriptionally silent. Thus using immunostaining techniques, we confirmed the occurrence of genome-wide DNA methylation changes during zebrafish embryogenesis, as well as observing the unique localisation of this mark around the nuclear periphery in conjunction with pericentric heterochromatin. For mono-, di- and tri-methylated H3K9, it was observed by both immunostaining and immunoblotting that these marks became apparent after the onset of zygotic transcription. Ultimately their levels increased as development progressed, in a fashion similar to that of DNA methylation, consistent with a link between these epigenetic marks. Using the same methodology, the three methylation states of H4K20 were seen to vary differentially during zebrafish development, where in particular the levels of H4K20me1 decreased in concert with a potentially sumoylated form. In contrast, the levels of H4K20me2 increased progressively during embryogenesis, while those of H4K20me3 decreased rapidly after the mid-blastula transition. Together, these findings demonstrate that both DNA and histone lysine methylation take place in a highly dynamic manner, further supporting their roles in augmenting chromatin structure and directing cellular differentiation, while also providing a valuable comparison to the developmental epigenetics of other model organisms characterised to date. Preparatory work for somatic cell nuclear transfer in zebrafish was also undertaken. In future studies, the dynamics of these marks could be compared with those of cloned embryos, so that the specific epigenetic profiles necessary for development can be elucidated. Epigenetically, a homologous process occurs within pluripotent embryonic stem cells (ESCs), which can differentiate into any cell type or undergo indefinite self-renewal. Advantageously, we were able to derive zebrafish ESC-like clusters which were morphologically similar to those derived from mice. These clusters were alkaline phosphatase-positive and expressed key ESC markers as detected by RT-PCR and immunofluorescence. In pilot studies, GFP-expressing ESC-like clusters have so far also contributed to ectodermal tissues when transplanted into wild type zebrafish embryos. Subsequently, these ESC-like clusters were epigenetically profiled using immunofluorescence, which showed that they had a similar complement of modifications to ESCs derived from mice. The derivation and initial characterisation of these ESC-like clusters from zebrafish, in addition to the development of somatic cell nuclear transfer in this species, will help pave the way for future studies involving tissue repair and regeneration, as well as opening up the potential of targeted genetic manipulation in this valuable model organism.