Gene expression patterns of epithelial cells modulated by pathogenicity factors of Yersinia enterocolitica

Epithelial cells express genes whose products signal the presence of pathogenic microorganisms to the immune system. Pathogenicity factors of enteric bacteria modulate host cell gene expression. Using microarray technology we have profiled epithelial cell gene expression upon interaction with Yersinia enterocolitica. Yersinia enterocolitica wild-type and isogenic mutant strains were used to identify host genes modulated by invasin protein (Inv), which is involved in enteroinvasion, and Yersinia outer protein P (YopP) which inhibits innate immune responses. Among 22 283 probesets (14,239 unique genes), we found 193 probesets (165 genes) to be regulated by Yersinia infection. The majority of these genes were induced by Inv, whose recognition leads to expression of NF-kappa B-regulated factors such as cytokines and adhesion molecules. Yersinia virulence plasmid (pYV)-encoded factors counter regulated Inv-induced gene expression. Thus, YopP repressed Inv-induced NF-kappa B regulated genes at 2 h post infection whereas other pYV-encoded factors repressed host cell genes at 4 and 8 h post infection. Chromosomally encoded factors of Yersinia, other than Inv, induced expression of genes known to be induced by TGF-beta receptor signalling. These genes were also repressed by pYV-encoded factors. Only a few host genes were exclusively induced by pYV-encoded factors. We hypothesize that some of these genes may contribute to pYV-mediated silencing of host cells. In conclusion, the data demonstrates that epithelial cells express a limited number of genes upon interaction with enteric Yersinia. Both Inv and YopP appear to modulate gene expression in order to subvert epithelial cell functions involved in innate immunity.     

盐胁迫下两个甜瓜品种转录因子的转录组分析

利用新一代高通量测序手段——转录组测序（RNA-Seq）技术研究在300 mmol.L-1NaCl胁迫下两个甜瓜（Cucumis melo L.）品种‘玉露’和‘冰雪脆’的转录因子基因表达变化。这两个甜瓜品种在叶绿素荧光参数上的差异表明其在盐胁迫下有不同的生理反应。转录组测序结果表明,盐胁迫与对照相比,‘玉露’共有属于19个转录因子家族的56个转录因子基因表达发生变化（在转录水平,属于7个转录因子家族的22个转录因子上调表达,属于14个转录因子家族的34个转录因子下调表达）。‘冰雪脆’有属于20个转录因子家族的47个转录因子基因表达发生变化（在转录水平上,属于5个转录因子家族的17个转录因子上调表达,属于17个转录因子家族的30个转录因子下调表达）。盐胁迫下,两个甜瓜品种差异表达的转录因子既表现特异性,也存在部分重叠。‘玉露’有29个转录因子特异响应,‘冰雪脆’有20个特异响应。盐胁迫响应重叠的转录因子有27个,其中9个上调表达,18个下调表达。采用实时荧光定量PCR对几个转录因子进行了盐胁迫下的表达检测,其趋势与转录组分析结果基本一致。     

用生物信息学方法寻找肝癌特异性表达基因转录调控模式

为了对肝癌(hepatocellularcarcinoma,HCC)的分子发病机理进行研究,首先对肝癌基因表达谱数据用t-检验算法进行了分析,找到了肝癌中特异性表达基因(characteristicgenes).然后把这些基因结合已知的肝HNF家族转录因子染色质免疫共沉淀结合DNA启动子芯片(ChIP-chip)实验数据用SAEM算法进行分析,得到了肝癌特异性表达基因的转录调控关系,并寻找到了多个HNF家族转录因子调控单基因的转录调控模式.结果表明HNF家族转录因子对大量具有重要功能的肝癌特异性表达基因进行了转录调控,并且多个HNF家族转录因子调控单基因可以形成前馈环和多输入调控等模式.     

Lipo-oligosaccharides of Rhizobium induce infection-related early nodulin gene expression in pea root hairs

This paper shows that lipo-oligosaccharides (Nod factors) synthesized by Rhizobium bacteria elicit the induction of infection-related early nodulin genes ( PsENOD5 and PsENOD12 ) in pea root hairs. R. leguminosarum bv. viciae secretes a mixture of Nod factors containing a C18 fatty acid chain with 4 (C18:4) or 1 double bond (C18:1). Purified Nod factors harbouring either a C18:4 or a C18:1 acyl moiety induce the expression of the pea early nodulin genes, PsENOD5 and PsENOD12 , but the kinetics of induction are different. The expression of both early nodulin genes is induced in a transient manner by the purified Nod factors while a mixture of the Nod factors extends the period during which these genes are expressed. In spite of the host-specific nature of the infection process, heterologous Nod factors of R. meliloti also induce the expression of PsENOD5 and PsENOD12 genes, though with a marked delay compared with the homologous compounds.     

神经管缺陷相关基因的研究进展

神经管缺陷是中枢神经系统最常见的先天畸形,许多种类基因的表达或突变与神经系统发育,神经管缺陷有关,它们是：（1）发育调节基因及转录因子类基因。（2）原癌基因和抑癌基因。（3）生长因子及其受体基因。（4）蛋白激酶C相关基因。（5）同型半胱氨酸代谢相关基因。（6）其他基因：细胞骨架类,细胞连接基因等。     

Platelet-derived growth factor-BB represses smooth muscle cell marker genes via changes in binding of MKL factors and histone deacetylases to their promoters

A hallmark of smooth muscle cell (SMC) phenotypic switching is suppression of SMC marker gene expression. Although myocardin has been shown to be a key regulator of this process, the role of its related factors, MKL1 and MKL2, in SMC phenotypic switching remains unknown. The present studies were aimed at determining if: 1) MKL factors contribute to the expression of SMC marker genes in cultured SMCs; and 2) platelet-derived growth factor-BB (PDGF-BB)-induced repression of SMC marker genes is mediated by suppression of MKL factors. Results of gain- and loss-of-function experiments showed that MKL factors regulated the expression of single and multiple CArG [CC(AT-rich)(6)GG]-containing SMC marker genes, such as smooth muscle (SM) alpha-actin and telokin, but not CArG-independent SMC marker genes such as smoothelin-B. Treatment with PDGF-BB reduced the expression of CArG-containing SMC marker genes, as well as myocardin expression in cultured SMCs, while it had no effect on expression of MKL1 and MKL2. However, of interest, PDGF-BB induced the dissociation of MKL factors from the CArG-containing region of SMC marker genes, as determined by chromatin immunoprecipitation assays. This dissociation was caused by the competition between MKL factors and phosphorylated Elk-1 at early time points, but subsequently by the reduction in acetylated histone H4 levels at these promoter regions mediated by histone deacetylases, HDAC2, HDAC4, and HDAC5. Results provide novel evidence that PDGF-BB-induced repression of SMC marker genes is mediated through combinatorial mechanisms, including downregulation of myocardin expression and inhibition of the association of myocardin/MKL factors with CArG-containing SMC marker gene promoters.     

整合冠心病风险SNPs功能及分子网络特征筛选疾病易感基因

目的:冠心病(Coronary Heart Disease,CHD)是一种由多因素(遗传因素、环境因素以及它们之间的相互作用)引起的复杂疾病。本文从遗传因素和分子互作模式识别新的冠心病易感基因。方法:结合冠心病群体遗传SNPs数据和PPI数据,通过群体遗传数据的风险评估、功能SNPs的判定和PPI网络基因的分类,以功能SNPs属性、网络拓扑属性和基因功能属性为特征,利用两步分类的方法筛选新的冠心病易感基因。结果:获得了69个新的冠心病易感基因,其中43个被文献证实与冠心病的发生发展密切相关,且识别的新的易感基因注释的KEGG通路中有很多是已知的易感基因所没有注释到的,如MAPK signaling pathway,Calcium signaling pathway,Focal adhesion和Chemokine signaling pathway等,其中Chemokine signaling pathway被证实是CHD发展的关键通路。结论:应用本文提出的整合筛选策略,能识别与冠心病相关的新的易感基因,可为冠心病的预防、诊断和治疗提供新的研究方向。     

转基因动物的乳腺表达

转基因动物乳腺组织特异性表达异源基因是近年来基因工程中引人注目的途径.文章介绍了这一途径有关的乳汁蛋白基因、乳汁蛋白基因与异源基因的融合方式、重组基因的必要构成以及可能影响高效表达的因素.