| Summary: | 博士 === 國立臺灣大學 === 基因體與系統生物學學位學程 === 105 === Epigenetic regulation describes multiple layers of signatures that are involved in governing the accessibilities of genomic regions. These signatures hence configure the gene expression patterns that define cell identity as well as drive cell fate decision. Additionally, epigenomes are mitotically heritable that serve to “remember” the differentiation progress and prepare for further modulation. Nevertheless, the relationships between epigenetic regulation and cell fate decision involved in many faces that have yet been understood. This thesis is comprised by two separate hypothesis, but all pointing to the understanding of spatiotemporal regulation of epigenome that lead to cell fate commitment. Here, chicken is used as the model organism in this thesis.
In my first project (chapter 2), given feather forming dorsal skin and scale forming metatarsal skin display dramatically different characteristics, but was found having interchangeable fate in early embryonic skin epithelium. How primal skins can develop into distinct features is becoming of interest. I hypothesize that region specific differentiation of skin epithelium cells is, at least partially, regulated by specific regulatory pathways and histone modification machineries triggered by mesenchymal signaling. In collaboration efforts, we applied unbiased cosine similarity analysis on 20 microarray expression profiles of undifferentiated and differentiated epithelium and mesenchymes for dorsal and metatarsal skin regions, and found genes involved calcium signaling pathway are regulated spatiotemporally regulated in association with each skin part in question. For investigation of cis enhancer activities associated with these genes, I successfully applied ChIP-seq for small number of cells and solved the limitation of low cell yields from undifferentiated skins. The result identified the enhancer signatures on calcium signaling pathway subunits are correlated with their gene expression, and in turn favor the fate decision toward scale-forming skins.
In the next project (chapter 3), I was focused in PIWI/piRNA pathway which is an important epigenetic regulatory machinery in silencing transposable elements (TEs) during germ cell development. Nevertheless, transcriptional regulation of piRNA cluster, which crucially shape piRNA profiles, was scarcely reported, particularly for piRNA clusters localized on intergenic regions. PiRNA clusters are transcribed by Pol II as for typical genes. I hypothesize some specific transcriptional factors may be involved in stage-dependent piRNA cluster regulations. In collaboration with colleagues, we designed and optimized bioinformatics pipeline for piRNA candidate filtering. I found transition of piRNA profiles from TE associated piRNAs to intergenic region orientated piRNAs along development from blastodermal cell to adult, which the result imply stage dependent regulation. Based on transcription factor binding site analysis, I identified some transcription factors may be involved in the developmental stage-dependent expression of piRNA clusters. The expression analysis further showed most of these transcription factors are also regulated in stage-dependent manner. In extension of this study, I found the stage-dependently regulated piRNAs in E11 and E14 male gonads are preferentially targeting to genes involved in neurogenesis. This finding imply expression repression, and therefore likely suppress cell fate development toward neuron lineages.
In summary, I applied systems biology perspective to both research arms, and identified two epigenetic regulatory features that likely contribute to epigenomic landscape for cell fate decision. These discoveries contribute to the further understanding of how epigenomic regulation may be involved for cell fate decision.
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