探討植物表觀基因體與轉錄體的動態調控

Abstract

植物的表觀基因體在發育的不同階段或面對逆境時發生變化，這些改變已知受到 特定遺傳因子調控，透過生物資訊以多體學的角度來描述遺傳因子和表觀基因體 間動態交互作用，能夠鉅細靡遺的看到過去單一基因座分析所不易彙整到的表觀 基因體變化。我的論文涵蓋了植物表觀基因體的四項主要領域:一、在逆境下的 反應與在水稻作物改良的應用，二、對發育的影響，三、在協同與拮抗調控中的 作用，以及四、對脂質生成和對其他物種的影響。在水稻轉殖過程中，複雜的組 織培養添加物對植物是逆境，轉殖過程改變了表觀基因體及外表性狀，使作物改 良實驗難以控制。我的研究目的在釐清整個複雜轉殖過程中會帶來的表觀基因體 變異。結果顯示轉殖過程中的數個重要轉殖因子對水稻造成全基因組 DNA 甲基 化與轉錄體的變化，其影響遠超過目前認為的組織培養。再者，我發現去泛素酶 的突變導致 H3K4me3 和 DNA 甲基化呈相反變化，從而影響與根發育和磷酸鹽 平衡相關的基因表達，作為植物面對低磷環境的適應反應。最後，我的研究進一 步延伸到探討一種組蛋白去乙醯化酶和另一種組蛋白去甲基化酶如何透過改變表 觀基因體以協同或拮抗方式調控跳耀子表達，而這兩種調控之間的轉換是由 H3Ac、H3K4me2 和 DNA 甲基化所操縱。在博士班期間，我也同時接觸了多個 物種的表觀遺傳研究，學習許多次世代實驗技術、設計與流程的建立。透過揭示 表觀基因體的動態與遺傳因子的相互作用，以及其在逆境下的反應與其對發育和 基因組穩定性的影響，我相信我的研究專注於植物表觀基因體調控，並貢獻於植 物生物學基礎研究和作物改良的潛在應用。

Plant epigenomes are shaped by specific genetic factors during development or in stress responses. Devising bioinformatic strategies to delineate dynamic interactions with a multi-omics perspective has great potential for new discoveries. My thesis emphasizes the major areas of plan epigenomics: 1. Epigenomic regulation under stress responses and its application in crop improvement, 2. Epigenomic regulation in development, 3. Epigenomic regulation in synergistic and antagonistic effects, and 4. Epigenomes in lipid production and in other species. In rice transformation, tissue culture is known to trigger epigenomic variations, resulting in phenotypic variations. I identified specific transformation treatments that impacted genome-wide DNA methylation associating with gene expression, beyond the effect from tissue culture. Stress conditions also trigger changes in histone modifications. I found that lacking a deubiquitinating enzyme led to anticorrelation in H3K4me3 and DNA methylation, influencing the expression of genes in root development and phosphate homeostasis, as responses to low phosphate. I further extended to uncover the synergistic regulation of transposable elements by a histone deacetylase and two demethylases. I found that the transition between synergistic and antagonistic regulations was jointly determined by H3Ac, H3K4me2 and DNA methylation types. I also joined several collaborative projects to explore epigenomes in other species and learned experimental skills. Overall, my PhD research of epigenomic regulation in plants uncovered the dynamic and interesting nature of epigenomes, their interplay with genetic factors, and their impacts on stress responses, development, and genome stability. I hope my thesis has contributed to both basic research in plant biology and potential applications in crop improvement.