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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 李文雄 | zh_TW |
| dc.contributor.advisor | Wen-Hsiung Li | en |
| dc.contributor.author | 陳麒安 | zh_TW |
| dc.contributor.author | Chi-An Chen | en |
| dc.date.accessioned | 2025-02-19T16:12:25Z | - |
| dc.date.available | 2025-02-20 | - |
| dc.date.copyright | 2025-02-19 | - |
| dc.date.issued | 2025 | - |
| dc.date.submitted | 2025-01-25 | - |
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| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/96490 | - |
| dc.description.abstract | 人類與其他靈長類的分化引起了廣泛關注,我們的重點在揭示推動人類特有特徵的基因和調控機制。本研究發現並鑑定了僅存在於人類中的轉錄因子(TF)與目標基因配對。通過利用高通量數據(如 ChIP-seq),我們預測了跨物種的 TF 結合位點。通過應用位置權重矩陣(PWMs)和 FIMO 軟體,我們鑑定了 844 對近端和 403 對遠端啟動子的人類特有 TF 與目標基因配對,分別獲得 320 和 231 個人類特有的近端和遠端目標基因,以及 246 和 231 個 TFs。
這些 TF 與目標基因配對通過人類腦類器官(cerebral organoids)和後扣帶皮質(posterior cingulate cortex)的基因表達數據進行驗證,揭示了人類與非人類靈長類之間的顯著表達差異。功能富集分析表明,這些配對高度相關於對腦部發育、神經系統功能和認知特化至關重要的生物過程。值得注意的例子包括 CNTN4 和 SEMA6D二基因,它們參與軸突導向和神經迴路的形成。 此外,通路分析強調了人類特有的 TF 與目標基因配對參與“Neurexins and Neuroligins”通路,這是一個調控突觸(synapse)組織與神經傳遞的關鍵調節器。例如,NLGN1 和 STXBP1 二基因表現出人類特有的調控變化與獨特的表達模式,暗示它們在塑造人類大腦功能複雜性方面的作用。 本研究提供了關於人類演化分子適應的關鍵見解。人類特有調控機制的鑑定為深入理解人類特有特徵(尤其是與高級神經與認知功能相關的特徵)的遺傳與表觀遺傳基礎提供了支持。 | zh_TW |
| dc.description.abstract | The conspicuous phenotypic divergences between humans and non-human primates have garnered much attention, aiming to uncover the genes and regulatory mechanisms driving human-specific trait developments. In this study, we identified transcription factor (TF) and target gene pairs that exist exclusively in humans but not in non-human primates. Utilizing high-throughput data such as ChIP-seq, we mapped TF binding sites in human and other primate genomes. By applying human position weight matrices (PWMs) and the FIMO software, we identified 844 proximal and 403 distal human-specific TF-target gene pairs, involving 320 and 231 target genes, respectively, that were associated with 246 and 231 TFs.
These TF-target gene pairs were evaluated using gene expression data from human and gorilla cerebral organoids and the human and non-human posterior cingulate cortexes, revealing many genes with significant expression differences between humans and non-human primates. Functional enrichment analysis indicated that these pairs are highly associated with biological processes crucial for brain development, nervous system development, and cognitive specialization. Notable examples include CNTN4 and SEMA6D, which are implicated in axon guidance and neural circuit formation. Moreover, pathway analysis highlighted the involvement of human-specific TF-target gene pairs in the "Neurexins and Neuroligins" pathway, a key pathway for synaptic organization and neurotransmission. Genes such as NLGN1 and STXBP1 exhibited human-specific regulatory changes and distinct expression patterns, suggesting their roles in shaping the complexity of human brain function. In summary, this study provides valuable insights into the molecular adaptations that underlie human evolution since its separation from the chimpanzee lineage. The identification of human-specific regulatory mechanisms offers a deeper understanding of the genetic foundations of uniquely human traits, particularly those related to advanced neural and cognitive functions. | en |
| dc.description.provenance | Submitted by admin ntu (admin@lib.ntu.edu.tw) on 2025-02-19T16:12:25Z No. of bitstreams: 0 | en |
| dc.description.provenance | Made available in DSpace on 2025-02-19T16:12:25Z (GMT). No. of bitstreams: 0 | en |
| dc.description.tableofcontents | 誌謝 I
中文摘要 II ABSTRACT III CHAPTER 1 1 Introduction 1 CHAPTER 2 4 Materials and Methods 4 2.1 Collection of human and non-human primate genomic data 4 2.2 Collection of human transcription factor PWMs 4 2.3 Processing of TF ChIP-seq data and TFBS validation 4 2.4 Inference of TF-target gene pairs 5 2.5 Handling Multiple TFBSs at the dame or nearby genomic locations 6 2.6 RNA-seq data of human and chimpanzee developing forebrain organoids of humans and gorillas 7 2.7 snRNA-Seq data from the posterior cingulate cortex in humans, chimpanzees, and macaques 8 2.8 Identifying human-specific genes on gene co-expression modules in eight brain regions 9 2.9 Statistical analysis 10 CHAPTER 3 10 Results 10 3.1 Predicted human specific TF-target gene pairs. 10 3.2 GO terms of predicted human-specific TF target genes 11 3.2.1 TF target genes potentially involved in nervous system development (GO:0007399) 12 3.2.2 TF target genes involved in neuron projection (GO:0043005) 13 3.2.3 TF target genes involved in cerebral cortex development (GO: 0021987) 13 3.2.4 TF target genes involved in positive regulation of synapse assembly (GO:0051965) 14 3.2.5 TF target genes involved in brain development (GO:0007420) 14 3.2.6 TF target genes involved in neuron differentiation (GO:0030182) 14 3.2.7 TF target genes involved in learning or memory (GO:0007611) 15 3.2.8 TF target genes involved in hippocampus development (GO:0021766) 15 3.2.9 TF target genes involved in cerebellum development (GO:0021549) 15 3.2.10 TF target genes involved in axon guidance (GO:0007411) 16 3.3 Overrepresented GO terms in human-specific proximal TF target genes 16 3.5 Human-specific TF target genes differentially expressed between human and gorilla developing cerebral organoids 16 3.6 Gene expression analysis in cerebral organoids using DESeq2 18 3.7 Enrichment of expressed human-specific proximal TF target genes in the human forebrain 21 3.8 Enrichment of differentially expressed human-specific proximal TF target genes in the human forebrain 21 3.9 Enrichment of differentially expressed genes among human-specific TF target genes expressed in the forebrain 22 3.10 Human-Specific TF target genes associated with the "Neurexins and Neuroligins" pathway 23 3.11 Human-specific TF target genes in gene co-expression modules of eight brain regions 24 3.12 Genes with human-specific regulation in the posterior cingulate cortex 26 CHAPTER 4 30 Discussion 30 4.1 Biological implications of human-specific regulation 30 4.2 Neural developmental differences among primates 31 4.3 Human-specific TFBS and co-expression modules: insights into evolutionary adaptations 32 4.4 Significance of Correlations Between Target Genes and Their Cognate TFs 32 4.5 Confirmed nervous system and brain development genes with human-specific TFBS in proximal promoters 33 4.6 Broader Implications for Brain Development and Evolution 34 4.7 Exploring the Functional Roles and Disease Links of Critical Genes 35 Figures 40 Tables 53 References 55 | - |
| dc.language.iso | en | - |
| dc.subject | 神經系統 | zh_TW |
| dc.subject | 啟動子 | zh_TW |
| dc.subject | 腦部 | zh_TW |
| dc.subject | 人類特有的潛在基因調控 | zh_TW |
| dc.subject | 轉錄因子 | zh_TW |
| dc.subject | promoter | en |
| dc.subject | transcription factor | en |
| dc.subject | human-specific potential gene regulation | en |
| dc.subject | brain | en |
| dc.subject | nervous system | en |
| dc.title | 推測人類特有的啟動子變化及其調控效應 | zh_TW |
| dc.title | Inferring human-specific promoter changes and their regulatory effects | en |
| dc.type | Thesis | - |
| dc.date.schoolyear | 113-1 | - |
| dc.description.degree | 博士 | - |
| dc.contributor.oralexamcommittee | 阮雪芬;陳倩瑜;莊樹淳;黃禎祥 | zh_TW |
| dc.contributor.oralexamcommittee | Hsueh-Fen Juan;Chien-yu Chen;Trees-Juen Chuang ;Chen-Siang Ng | en |
| dc.subject.keyword | 轉錄因子,人類特有的潛在基因調控,腦部,神經系統,啟動子, | zh_TW |
| dc.subject.keyword | transcription factor,human-specific potential gene regulation,brain,nervous system,promoter, | en |
| dc.relation.page | 61 | - |
| dc.identifier.doi | 10.6342/NTU202500276 | - |
| dc.rights.note | 同意授權(限校園內公開) | - |
| dc.date.accepted | 2025-01-25 | - |
| dc.contributor.author-college | 生命科學院 | - |
| dc.contributor.author-dept | 基因體與系統生物學學位學程 | - |
| dc.date.embargo-lift | 2030-01-22 | - |
| 顯示於系所單位: | 基因體與系統生物學學位學程 | |
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