From raw materials to validated system: the construction of a genomic library and microarray to interpret systemic perturbations in Northern bobwhite
From raw materials to validated system: the construction of a genomic library and microarray to interpret systemic perturbations in Northern bobwhite
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DOI：
10.1152/physiolgenomics.00022.2010
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发表时间：
2010-07-01
影响因子：
4.6
通讯作者：
Perkins, Edward J.
中科院分区：
文献类型：
--
作者：
Rawat, Arun;Gust, Kurt A.;Perkins, Edward J.
Rawat A，Gust KA，Deng Y，Garcia-Reyero N，Quinn MJ Jr，约翰约翰逊MS，Indest KJ，Elasri MO，Perkins EJ.从原材料到验证系统：构建基因组文库和微阵列来解释北方白山雀的系统扰动。Physiol Genomics 42：219-235，2010.首次发表于2010年4月6日; doi：10.1152/physiolgenomics.00022.2010.-非模式物种的基因组工具和数据的有限性阻碍了非模式生物的计算和系统生物学方法。在这里，我们描述的发展，功能注释，并利用基因组工具的鸟类野生动物物种北方bobwhite（Colinus virginianus），以确定暴露于2，6-二硝基甲苯（2，6-DNT），一个领域的军事污染物的分子影响。对北方山雀cDNA的标准化多组织文库进行大规模并行焦磷酸测序，得到71，384个独特的转录物，这些转录物用基因本体（GO）、途径信息和蛋白质结构域分析进行注释。与模式生物的比较基因组分析揭示了8，825个独特的北方山鸡基因的功能同源性，这些基因与原鸡蛋白质编码基因的48%是直系同源的。在暴露于10和60 mg/kg/d 2，6-DNT 60天（d）的鸟类肝脏中差异表达的基因的途径分析和GO富集揭示了通过RT-qPCR验证的几种影响，包括：前列腺素途径介导的炎症，响应贫血的血红素合成途径的表达增加，以及通过抑制葡萄糖和脂质代谢途径的控制点，分别为PCK 1和PPARGC 1，使能量代谢向蛋白质代谢的转变。这项研究工作提供了第一个全面的注释基因库北方鲍。转录表达分析提供了对2，6-DNT暴露案例研究中观察到的几种毒理学表型的代谢扰动的见解。此外，二硝基甲苯对肝功能的全身影响似乎在物种间是保守的，因为暴露于2，4-DNT后，黑头呆鱼肝脏组织中的PPAR信号传导也受到类似的影响。
Rawat A, Gust KA, Deng Y, Garcia-Reyero N, Quinn MJ Jr, Johnson MS, Indest KJ, Elasri MO, Perkins EJ. From raw materials to validated system: the construction of a genomic library and microarray to interpret systemic perturbations in Northern bobwhite. Physiol Genomics 42: 219-235, 2010. First published April 6, 2010; doi: 10.1152/physiolgenomics.00022.2010.-The limited availability of genomic tools and data for nonmodel species impedes computational and systems biology approaches in nonmodel organisms. Here we describe the development, functional annotation, and utilization of genomic tools for the avian wildlife species Northern bobwhite (Colinus virginianus) to determine the molecular impacts of exposure to 2,6-dinitrotoluene (2,6-DNT), a field contaminant of military concern. Massively parallel pyrosequencing of a normalized multitissue library of Northern bobwhite cDNAs yielded 71,384 unique transcripts that were annotated with gene ontology (GO), pathway information, and protein domain analysis. Comparative genome analyses with model organisms revealed functional homologies in 8,825 unique Northern bobwhite genes that are orthologous to 48% of Gallus gallus protein-coding genes. Pathway analysis and GO enrichment of genes differentially expressed in livers of birds exposed for 60 days (d) to 10 and 60 mg/kg/d 2,6-DNT revealed several impacts validated by RT-qPCR including: prostaglandin pathway-mediated inflammation, increased expression of a heme synthesis pathway in response to anemia, and a shift in energy metabolism toward protein catabolism via inhibition of control points for glucose and lipid metabolic pathways, PCK1 and PPARGC1, respectively. This research effort provides the first comprehensive annotated gene library for Northern bobwhite. Transcript expression analysis provided insights into the metabolic perturbations underlying several observed toxicological phenotypes in a 2,6-DNT exposure case study. Furthermore, the systemic impact of dinitrotoluenes on liver function appears conserved across species as PPAR signaling is similarly affected in fathead minnow liver tissue after exposure to 2,4-DNT.