Differentially expressed zinc finger proteins during human adipogenesis

To investigate the collective role of zinc finger proteins in adipogenesis, we induced adipogenesis using human mesenchymal stem cells (MSC) and compared the gene expression profiles using human Illumina beads arrays. We performed three independent experiments of time-series analysis (0h, 1h, 12h, 24h, 2d, 4d, 6d, 9d, 12d, 15d after induction of adipogenesis) in order to comprehensively capture the dynamic profiles of transcriptome during differentiation. Statistical filtering based on Analysis of Variance (ANOVA; p-value < 0.001, FDR 5%) and Gene Ontology classification using the Human Gene Nomenclature Database (HGNC) identified 618 out of 678 zinc finger proteins (ZFPs) that were significantly expressed during adipogenesis. Moreover, 34 out of 618 genes were differentially expressed more than 2-fold up or down regulated. The K-means clustering analysis further revealed four dynamic expression patterns: one gene in early-response, seven genes in transient, twenty genes in progressively-induced and four genes in the down-regulated, demonstrating the dynamic involvement of ZFPs in the process of adipocyte differentiation and maturation. Total RNA obteind from 10 different time points (0h, 1h, 12h, 24h, 2d, 4d, 6d, 9d, 12d, 15d) during adipogenesis from human Mesenchymal stem cell (MSC) to Adipocyte (ADP). Adipogensis was induced by the different cocktail of chemical compunds containing human-insulin, dexamethasone, indomethacin and IBMX.

为探究锌指蛋白（zinc finger proteins, ZFPs）在脂肪生成过程中的集体调控作用，我们以人间充质干细胞（human mesenchymal stem cells, MSC）为模型诱导脂肪生成，并采用人类Illumina微珠芯片（Illumina beads arrays）分析并比较基因表达谱。为全面捕获细胞分化过程中转录组的动态变化特征，我们开展了3组独立的时间序列转录组分析实验，采样时间点覆盖脂肪生成诱导后的0h、1h、12h、24h、2d、4d、6d、9d、12d、15d。基于方差分析（Analysis of Variance, ANOVA；p值<0.001，错误发现率（False Discovery Rate, FDR）5%）的统计筛选，结合依托人类基因命名委员会数据库（Human Gene Nomenclature Database, HGNC）完成的基因本体（Gene Ontology, GO）注释分类，我们从678个锌指蛋白基因中筛选出618个在脂肪生成过程中显著表达的基因。进一步分析显示，该618个基因中有34个的表达量出现了2倍以上的上调或下调差异。K均值聚类（K-means clustering）分析进一步揭示了4种动态表达模式：早期应答型1个、瞬时表达型7个、渐进诱导型20个以及下调型4个，这证实锌指蛋白在脂肪细胞分化与成熟过程中存在动态参与调控的作用。本数据集的总RNA样本提取自人间充质干细胞向脂肪细胞（adipocyte, ADP）分化过程中的10个时间点：0h、1h、12h、24h、2d、4d、6d、9d、12d、15d。脂肪生成过程通过包含人胰岛素、地塞米松、吲哚美辛与3-异丁基-1-甲基黄嘌呤（IBMX）的复合化学诱导液进行诱导。