推測人類特有的啟動子變化及其調控效應

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。

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.