不同细胞中STAT元件对刺激因子的特异性应答

以高通量药物筛选为目的,构建转录因子STAT元件驱动的萤火虫荧光素酶报告载体,并进行功能初步验证.人工合成含IRF－1和C－FOS基因上游调控序列中的2个STAT元件的DNA片段,克隆于pGL3－promoter报道质粒作为报道载体pSTAT luc|为检测其对不同有效因子刺激的反应性,该报道载体与荧光内参照载体pRL－SV40瞬时共转染不同细胞,在各种因子刺激条件下,双荧光素酶检测系统测定化学发光强度. 结果显示,pSTAT－luc的报道基因载体符合预期设计|该载体转染细胞实验显示,在STAT途径阳性的HeLa、A549和MCF 7细胞中,特异刺激因子INF－γ和抑瘤素OSM处理能够剂量依赖性的引起细胞内萤火虫荧光素酶的升高|在STAT途径阴性的PC－12细胞,上述因子不能引起荧光素酶的活性改变|以非该途径因子刺激时,HeLa、A549和MCF－7细胞未见发光水平的改变.结果表明,构建的报道系统具有阳性细胞反应特异性以及阳性刺激 反应特异性,能够用于建立靶向STAT信号通路的高通量药物筛选平台.     

Inflammatory cytokines regulate microRNA-155 expression in human retinal pigment epithelial cells by activating JAK/STAT pathway

Inflammatory response of the retinal pigment epithelium plays a critical role in the pathogenesis of retinal degenerative diseases such as age-related macular degeneration. Our previous studies have shown that human retinal pigment epithelial (HRPE) cells, established from adult donor eyes, respond to inflammatory cytokines by enhancing the expression of a number of cytokines and chemokines. To investigate the role of microRNA (miRNA) in regulating this response, we performed microarray analysis of miRNA expression in HRPE cells exposed to inflammatory cytokine mix (IFN-γ + TNF-α + IL-1β). Microarray analysis revealed ∼11-fold increase in miR-155 expression, which was validated by real-time PCR analysis. The miR-155 expression was enhanced when the cells were treated individually with IFN-γ, TNF-α or IL-1β, but combinations of the cytokines exaggerated the effect. The increase in miR-155 expression by the inflammatory cytokines was associated with an increase in STAT1 activation as well as an increase in protein binding to putative STAT1 binding elements present in the MIR155 gene promoter region. All these activities were effectively blocked by JAK inhibitor 1. Our results show that the inflammatory cytokines increase miR-155 expression in human retinal pigment epithelial cells by activating the JAK/STAT signaling pathway.     

核小体定位模式及其与DNA甲基化位点分布的关系

核小体定位是指DNA双螺旋相对于组蛋白八联体的位置.核小体定位通过限制蛋白结合位点参与基因转录调控.本文利用实验检测的人类CD4+ T细胞核小体定位数据,研究了核小体定位在转录因子结合位点(TFBS)和转录起始位点(TSS)附近的分布模式,并分析了在TFBS和TSS周围,核小体定位与DNA甲基化之间的关系.结果表明,在休眠和激活的人类CD4+ T细胞中,部分TFBS和TSS周围的核小体定位在动态改变,即在定位和缺失两种状态之间切换.在TFBS周围,核小体定位和DNA甲基化存在一种互补模式,核小体定位与DNA低甲基化相联系;而在TSS周围,两者呈现同步模式,DNA高甲基化伴随高核小体水平.而且,在TFBS和TSS周围,DNA甲基化位点的分布呈周期模式.CD4+ T细胞被激活时,较少的转录因子启动了较多的基因.     

LinkNMF: Identification of histone modification modules in the human genome using nonnegative matrix factorization

Histone modifications are ubiquitous processes involved in various cellular mechanisms. Systemic analysis of multiple chromatin modifications has been used to characterize various chromatin states associated with functional DNA elements, gene expression, and specific biological functions. However, identification of modular modification patterns is still required to understand the functional associations between histone modification patterns and specific chromatin/DNA binding factors. To recognize modular modification patterns, we developed a novel algorithm that combines nonnegative matrix factorization (NMF) and a clique-detection algorithm. We applied it, called LinkNMF, to generate a comprehensive modification map in human CD4 + T cell promoter regions. Initially, we identified 11 modules not recognized by conventional approaches. The modules were grouped into two major classes: gene activation and repression. We found that genes targeted by each module were enriched with distinguishable biological functions, suggesting that each modular pattern plays a unique functional role. To explain the formation of modular patterns, we investigated the module-specific binding patterns of chromatin regulators. Application of LinkNMF to histone modification maps of diverse cells and developmental stages will be helpful for understanding how histone modifications regulate gene expression. The algorithm is available on our website at biodb.kaist.ac.kr/LinkNMF.