玉米是重要的糧食及生質能源作物。在科學研究上，它是C4光合作用原理研究上的重要模式物種。在2009年，它的基因體(genomes)被定序而公開出來。在高通量定序及生物資訊技術越來越先進之下，玉米的基因體及轉錄體(transcriptomes)的資訊越來越豐富並且足夠用來進行各種組織細胞發育以及面對不同內在外在環境刺激的基因表現的巨觀研究。然而關於調控基因體學(regulatory genomics)研究的資料還是相當缺乏的。
調控基因體學是研究基因體中調控基因表現的功能元素與他們的調控者的關係的研究領域。為了瞭解一個物種調控基因體學的知識，我們必須知道它的轉錄因子(transcription factors，簡稱TFs)、轉錄共同調控因子(transcription coregulators簡稱TCs)、轉錄因子結合位點(transcription factor binding sites，簡稱TFBSs)以及轉錄因子與結合位點的關係(TF-TFBS relationships)。本論文著重玉米調控基因體學之各種重要的元素的研究。
在這研究上我設計了一系列生物資訊的方法。首先我鑑定了玉米中2538個轉錄因子基因以及149個轉錄共同調控因子基因。因為小米跟玉米一樣是重要的C4光合作用模式物種，所以我也鑑定了小米Yugu1品系的1880個轉錄因子基因以及99個轉錄共同調控因子基因，還有張谷品系的1846個轉錄因子基因及104個轉錄共同調控因子基因。我發現90%以上的玉米及小米的轉錄因子基因以及轉錄共同調控因子基因在阿拉伯芥或水稻都有同源基因，而至少75%以上的玉米及小米的轉錄因子基因以及轉錄共同調控因子基因都可以在轉錄體資料中知道它們是有表現的。我比較了他們在各組織轉錄體資料的表現量，也在玉米發現了995個轉錄因子基因以及71個轉錄共同調控因子基因跟C4光合作用的特徵可能有關，同時在小米中發現了546個轉錄因子基因以及33個轉錄共同因子基因可能跟C4光合作用有關。
接著我跟游竣評博士合作，整合了玉米基因體及葉片發育的轉錄體資料，預測了跟葉片發育相關的轉錄因子結合位點、還有他們對應的轉錄因子。我們假設轉錄因子基因跟下游基因的表達是同步的、相同功能的基因必須有同樣的轉錄因子結合位點、有作用的轉錄因子結合位點必須也在相近物種的同源基因存在、及演化上同源的轉錄因子也會有相近的轉錄因子結合位點。我們找到了239個玉米轉錄因子及結合位點的配對，他們對應到135個不重複的玉米轉錄因子，預測方法的成功率是76%。我的論文整合了從上游的轉錄因子跟轉錄共同調控因子的鑑定，到下游在玉米葉片發育過程中轉錄因子與結合位點的關聯性的分析，這些資訊也會幫助我們了解C4光合作用跟C4植物葉片花環結構發育的調控網路。

Maize (Zea mays) is an important crop and feedstock of biofuel. It is also a common model plant for studying the biology of C4 photosynthesis and the development of kranz anatomy, a key structure in C4 plant leaves. Its genome was sequenced in 2009. Through advances in DNA sequencing technologies and bioinformatics skills, genomic and transcriptomic information in maize has become abundant and has facilitated large-scale studies greatly. However, knowledge on the regulatory genomics in the 2GB maize genome is still very limited.
Regulatory genomics is the study of the relationship between functional elements and their regulators in a genome. Thus, to study the regulatory genomics of an organism, we need to identify the transcription factors (TFs), transcription coregulators (TCs), transcription factor binding sites (TFBSs) and TF-TFBS relationships. I aimed at gaining a good understanding of the regulatory genomics of maize, from which one can dissect the key regulatory features.
I designed bioinformatics methods to study each aspect of the regulatory genomics in maize leaf development. My main focuses are the construction of the modules consisting of TF and TC gene, TFBSs and TF-TFBS pairs. I first annotated 2538 TF genes and 149 TC genes in maize. Because millet (Setaria italica) is another important C4 plant, I also annotated 1880 TF genes and 99 TC genes in millet Yugu1, and 1846 TF genes and 104 TC genes in millet Zhang gu. I provided supporting evidence for my predictions of TF and TC genes from gene expression data in maize or millet and from homologous genes in Arabidopsis or rice. I found that more than 90% of TF and TC genes in maize and millets have homologs in Arabidopsis or rice and more than 75% of maize and millet TF and TC genes were expressed. I evaluated the expression preference of TF and TC genes in tissues in maize and millet and identified 995 TF genes and 71 TC genes in maize and 546 TF genes and 33 TC genes in millet that may potentially contribute to C4 characteristics in the two species.
I then collaborated with Dr. Chun-Ping Yu and developed a method that can identify the TFBSs in maize genome by integrating the time-course RNA-seq transcriptome of maize leaf development, maize genome sequence data and available TF-TFBS pairs in other species. We assumed that the TF genes should be coexpressed with their target genes, genes with the same function should possess the same TFBSs and regulated by the same TFs, the functional TFBSs should be conserved in closely related species, and the homologous TFs should still possess similar DNA-binding specificities. We identified 239 maize TF-TFBS pairs for 135 nonredundant maize TFs, achieving a prediction rate of 76%.
My study provides the overall work from characterization of TFs and TCs to the TF-TFBS relationship in maize leaf development and the basis for understanding the regulatory network of C4 photosynthesis and Kranz anatomy.

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