HOXC9-induced neuronal differentiation in human neuroblastoma BE(2)-C cells [ChIP-seq analysis]. Homo sapiens

Cell differentiation is an essential process of normal development by which a stem cell or progenitor cell becomes a post-mitotic, specialized cell with unique morphology and function. Also, it has long been recognized that differentiation is associated with a marked reduction in DNA damage response at the global level. The molecular basis for the coordination between cell cycle exit, acquirement of specialized structure and function, and attenuation of DNA damage response during differentiation is not well understood. We have conducted a genome-wide analysis of the HOXC9-induced neuronal differentiation program in human neuroblastoma cells. Gene expression profiling reveals that HOXC9-induced differentiation is associated with transcriptional regulation of 2,395 genes, which is characterized by global upregulation of neuronal genes and downregulation of cell cycle and DNA repair genes. Remarkably, genome-wide mapping demonstrates that HOXC9 occupies 40% of these genes, including a large number of genes involved in neuronal differentiation, cell cycle progression and DNA damage response. These findings suggest that HOXC9 directly activates and represses the transcription of distinct sets of genes to coordinate the cellular events characteristic of neuronal differentiation. Overall design: Two independent preparations of BE(2)-C/Tet-Off/Myc-HOXC9 cells cultured in the absence of doxycycline for 6 days were used for chromatin immunoprecipitation (ChIP) against Myc-tagged HOXC9 and massively parallel sequencing by Illumina Genome Analyzer IIx.

细胞分化（Cell differentiation）是正常发育的核心过程，指干细胞或祖细胞最终分化为具有独特形态与功能的有丝分裂后特化细胞。此外，学界长期以来已达成共识：细胞分化在全局水平上与DNA损伤应答（DNA damage response）的显著减弱密切相关。目前，学界对于细胞分化过程中细胞周期退出、特化结构与功能获得，以及DNA损伤应答减弱这几类事件的协同调控分子机制仍缺乏充分认知。本研究针对人神经母细胞瘤细胞中HOXC9诱导的神经元分化程序开展了全基因组水平分析。基因表达谱分析结果显示，HOXC9诱导的分化过程与2395个基因的转录调控密切相关，其核心特征为神经元基因的全局上调，以及细胞周期与DNA修复基因的全局下调。值得注意的是，全基因组定位分析结果表明，HOXC9可结合其中40%的基因，其中包含大量参与神经元分化、细胞周期进程及DNA损伤应答的基因。上述研究结果表明，HOXC9可通过直接激活与抑制不同基因集的转录，协同调控神经元分化特征性的各类细胞事件。实验整体设计：本研究采用两批独立培养的BE(2)-C/Tet-Off/Myc-HOXC9细胞，在不含多西环素（doxycycline）的培养基中培养6天后，针对带有Myc标签的HOXC9进行染色质免疫共沉淀（chromatin immunoprecipitation, ChIP），并通过Illumina Genome Analyzer IIx平台开展大规模平行测序。