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Genome-wide screening of dioxin-responsive genes

二恶英响应基因的全基因组筛选

基本信息

批准号：
15591162
负责人：
KOSAKI Kenjiro
金额：
$ 2.11万
依托单位：
Keio University
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (C)
财政年份：
2003
资助国家：
日本
起止时间：
2003 至 2004
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-15591162/
关键词：
dioxin TCDD endocrine disruptors microarray brain teratogen

项目摘要

Dioxins alter the expression levels of downstream target genes and affect development and differentiation through the aryl hydrocarbon receptor. However, the spectrum of the dioxin-responsive genes is yet to be delineated. The purpose of the present study is to define the spectrum of dioxin-responsive genes in a comprehensive manner using two complementary approaches : bioinformatic analysis and micro-array analysis.First, we mapped the xenobiotics responsive elements[XREs] within the putative promoter regions[PPRs] in a semi genome-wide manner. XREs are the consensus transcriptional regulation sequence "gcgtg" which are present in the PPRs of several genes induced by dioxins. Human analysis Sequences 10kb upstream from the transcription start sites[TSSs] of 2,773 genes were obtained by aligning 8,060 cDNA sequences in the human full-length cDNA database of The Institute of Medical Science with the human genome sequences 2,843 out of 2,773 genes possessed at least three XRE consensus s … More equences(gcgtg) within 10kb upstream of the TSS. Total number of XREs within the PPR was 26,787 among the 2,773 genes. The position of the 26,787 XREs from the TSS was ploteted on Fig. 2a. The XRE tended to be present closer to the TSS. The position of the smallest duster among all the XRE dusters within each 10kb upstream sequence tended to be present near the TSS. Mouse analysis : Sequences 10kb upstream from the TSSs of 18,541 genes were obtained by aligning 60,770 cDNA sequences in the FANTOM2 mouse full-length cDNA database of with the mouse genome sequences. 9,762 out of 18,541 genes possessed at least three XRE consensus sequences within 10kb upstream of the TSS. Total number of XREs within the PPR was 74,725 among the 9,762 genes. Again, in mice, the XRE tended to be present closer to the TSS. The position of the smallest cluster among all the XRE clusters within each 10kb upstream sequence trended to be present near the TSS.Second, we evaluated the expression profile of the mouse embryonic brain exposed to the prototypic dioxin, 2,3,7,8-tetrarchlorodibenzo-p-dioxin (TCDD), and compared with the expression profile of the unexposed brain. The expression values for the 6 hybridizations(3 from experimental group and 3 from the control group) were background-subtracted and normalized. We inferred genes that differentially expressed under TCDD exposure using a robust data-driven method. About 0.37%(46/12488) of the assessed genes showed significant(p<0.0001) change, either increase or decrease, in gene expression(Table 1). Among the 40 genes, 22 genes increased and 24 genes decreased their expression in TCDD-exposed pup brain. Cyp1b1 and Cyp1a1, both of which have been shown previously to be induced by dioxin exposure in vitro, were induced in the list. The changes in the expression level were plotted against the average intensity and the Bonferroni-style gene by gene tests were performed to determine the critical interval. Some of genes down-regulated by dioxin exposure are disease-causing genes : Mid1, Pitx2, and Gata3. Mutations in those genes lead to Opitz syndrome, Rieger syndrome, and HDR syndrome, respectively. Mutation in human MID1 gene is known to cause cleft palate, a cardinal feature of prenatal dioxin exposure in mice. In addition, Glyoxalase 1 (GLO) was down-regulated in the exposed group. A reduction in GLO1 enzyme activity has been demonstrated to result in the accumulation of methylglyoxal, which may be toxic to the developing brain Furthermore, an association study revealed that single nucleotide polymorphism in glyoxalase I as autism susceptibility factor (Junaid et al., 2004). In view of a potential role of xenobiotic toxins in the development of autistic spectrum (Edelson and Cantor, 1998), the biological relevance of GLO1 reduction in the exposed group needs to be further explored. Less

二恶英改变下游靶基因的表达水平，并通过芳烃受体影响发育和分化。然而，二恶英反应基因的谱尚待划定。本研究的目的是利用生物信息学分析和微阵列分析这两种互补的方法，全面地确定二恶英反应基因的谱。首先，我们以半基因组的方式定位了推定的启动子区域[PPRs]内的外源性物质反应元件[XREs]。XRE是存在于二恶英诱导的几个基因的PPR中的共有转录调控序列“gcgtg”。人类分析通过将医学科学研究所的人类全长cDNA数据库中的8，060个cDNA序列与人类基因组序列进行比对，获得了2，773个基因的转录起始位点（TSS）上游10 kb的序列，其中2，843个基因具有至少3个XRE共有序列。 ...更多信息 TSS上游10 kb内的序列（gcgtg）。PPR内的XRE总数为26，787，在2，773个基因中。来自TSS的26，787个XRE的位置绘制在图2a上。XRE倾向于更靠近TSS。在每个10 kb上游序列中的所有XRE簇中，最小的簇的位置倾向于出现在TSS附近。小鼠分析：通过将FANTOM 2小鼠全长cDNA数据库中的60，770个cDNA序列与小鼠基因组序列进行比对，获得了18，541个基因的TSS上游10 kb的序列。在18，541个基因中，有9，762个基因在TSS上游10 kb内至少有3个XRE共有序列。PPR内的XRE总数为9，762个基因中的74，725个。同样，在小鼠中，XRE倾向于更接近TSS。第二，我们研究了原型二恶英2，3，7，8-四氯二苯并-对-二恶英（TCDD）暴露于小鼠胚胎脑中的表达谱，并与未暴露的小鼠胚胎脑中的表达谱进行了比较。将6次杂交（3次来自实验组，3次来自对照组）的表达值减去背景并标准化。我们使用一个强大的数据驱动的方法推断TCDD暴露下差异表达的基因。约0.37%（46/12488）的评估基因显示出基因表达的显著（p<0.0001）变化，增加或减少（表1）。在40个基因中，22个基因在TCDD暴露的幼鼠脑中表达增加，24个基因表达减少。Cyp 1b 1和Cyp 1a 1，这两个都已被证明是诱导二恶英暴露在体外，在列表中诱导。将表达水平的变化相对于平均强度作图，并进行Bonferroni型基因的基因测试以确定临界区间。一些被二恶英暴露下调的基因是致病基因：Mid 1，Pitx 2和Gata 3。这些基因的突变分别导致Opitz综合征、Rieger综合征和HDR综合征。人类MID 1基因突变已知会导致腭裂，这是小鼠产前暴露于二恶英的主要特征。此外，暴露组中的Glycosidase 1（GLO）下调。已经证明GLO 1酶活性的降低导致甲基乙二醛的积累，甲基乙二醛可能对发育中的大脑有毒。此外，相关研究表明，作为自闭症易感因子的谷胱甘肽酶I的单核苷酸多态性（Junaid et al.，2004年）。鉴于外源性毒素在自闭症谱系发展中的潜在作用（Edelson和Cantor，1998年），需要进一步探讨接触组中GLO 1减少的生物相关性。少