MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China.
Genomics. 2012 Nov;100(5):297-302. doi: 10.1016/j.ygeno.2012.07.009. Epub 2012 Jul 21.
Gene expression is a dynamic process, and what factors influence gene expression changes upon external stimulus have not been clearly understood. We studied gene expression profiles in human umbilical vein endothelial cells (HUVEC) after the Tumor Necrosis Factor (TNF) stimulus, and found that: the promoters of fast-response up-regulated genes were enriched with several "active" chromatin markers like H3K27ac and H3K4me3, and also preferentially bound by Pol II and c-Myc; the core-promoter regions of slow-response up-regulated genes were frequently occupied by nucleosomes; down-regulated genes were more intensively regulated by microRNAs. Moreover, the Gene Ontology and motif analysis of the promoter regions revealed that gene clusters with different response behaviors had different functions and were regulated by different sets of transcription factors. Our observations suggested that the different gene expression patterns upon external stimulus were regulated by a combination of multi-layer regulators.
基因表达是一个动态的过程，对于外界刺激如何影响基因表达变化的因素还不是很清楚。我们研究了肿瘤坏死因子（TNF）刺激后人类脐静脉内皮细胞（HUVEC）中的基因表达谱，发现：快速反应上调基因的启动子富含几种“活跃”的染色质标记，如 H3K27ac 和 H3K4me3，也优先与 Pol II 和 c-Myc 结合；缓慢反应上调基因的核心启动子区域经常被核小体占据；下调基因受到 microRNAs 的更密集调控。此外，启动子区域的基因本体论和基序分析表明，具有不同反应行为的基因簇具有不同的功能，并受到不同转录因子集的调控。我们的观察结果表明，不同的基因表达模式受到多种调控因子的组合调控。
