RNA-Seq reveals complex genetic response to Deepwater Horizon oil release in Fundulus grandis.
RNA-Seq reveals complex genetic response to Deepwater Horizon oil release in Fundulus grandis.
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DOI：
10.1186/1471-2164-13-474
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发表时间：
2012-09-12
期刊：
影响因子：
4.4
通讯作者：
Walter RB
中科院分区：
文献类型：
--
作者：
Garcia TI;Shen Y;Crawford D;Oleksiak MF;Whitehead A;Walter RB
深水地平线（DH）钻井平台井喷造成的石油泄漏是历史上最大的石油泄漏之一，排放了超过1.89亿加仑的石油，并受到石油分散剂的广泛应用。这一事件影响了广泛的生态栖息地，污染物的复杂组合，其生物影响尚未完全了解。为了更好地了解对脊椎动物基因组的影响，我们研究了盐沼小鱼Fundulus grandis的基因表达，这是当地的墨西哥湾北方海岸，是生态毒理学模型Fundulus heteroclitus的姐妹物种。为了评估基因组的变化，我们使用高通量测序技术（RNA-Seq）在F.受DH石油释放影响的沼泽和河口的grandis种群。将RNA-Seq应用于非模型、野生和具有生态意义的生物体是对该技术的重要评估，以在未来快速评估类似事件。我们的从头组装RNA-Seq数据产生了一个大的序列集，其中包括许多重复和片段。在许多情况下，这些中的几个可以与使用blast查询参考数据库的共同参考序列相关联。这将显著基因组减少到1，070个下调基因和1，251个上调基因。这些基因表明对DH油暴露的广泛而复杂的基因组应答，包括预期的AHR介导的应答和EhrB基因。此外，还表明了对缺氧条件的应答和免疫应答。在暴露组中，绒毛膜生长素家族中的几个基因下调;这一反应与AH暴露一致。这些分析是在协议与阿托伐他汀为基础的微阵列分析，并描述了只有一个子集的显着基因与异常调控的曝光集。RNA-Seq可以成功地应用于野生的和极其多态的生物体，这些生物体没有潜在的基因组序列组装，以及时解决环境问题。此外，观察到的大量转录本表达水平的变化表明了对鱼类所暴露的各种石油成分的复杂反应。
The release of oil resulting from the blowout of the Deepwater Horizon (DH) drilling platform was one of the largest in history discharging more than 189 million gallons of oil and subject to widespread application of oil dispersants. This event impacted a wide range of ecological habitats with a complex mix of pollutants whose biological impact is still not yet fully understood. To better understand the effects on a vertebrate genome, we studied gene expression in the salt marsh minnow Fundulus grandis, which is local to the northern coast of the Gulf of Mexico and is a sister species of the ecotoxicological model Fundulus heteroclitus. To assess genomic changes, we quantified mRNA expression using high throughput sequencing technologies (RNA-Seq) in F. grandis populations in the marshes and estuaries impacted by DH oil release. This application of RNA-Seq to a non-model, wild, and ecologically significant organism is an important evaluation of the technology to quickly assess similar events in the future. Our de novo assembly of RNA-Seq data produced a large set of sequences which included many duplicates and fragments. In many cases several of these could be associated with a common reference sequence using blast to query a reference database. This reduced the set of significant genes to 1,070 down-regulated and 1,251 up-regulated genes. These genes indicate a broad and complex genomic response to DH oil exposure including the expected AHR-mediated response and CYP genes. In addition a response to hypoxic conditions and an immune response are also indicated. Several genes in the choriogenin family were down-regulated in the exposed group; a response that is consistent with AH exposure. These analyses are in agreement with oligonucleotide-based microarray analyses, and describe only a subset of significant genes with aberrant regulation in the exposed set. RNA-Seq may be successfully applied to feral and extremely polymorphic organisms that do not have an underlying genome sequence assembly to address timely environmental problems. Additionally, the observed changes in a large set of transcript expression levels are indicative of a complex response to the varied petroleum components to which the fish were exposed.
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转录组对芳基烃受体（AHR）激动剂在大西洋Killifish（heteroclitus）胚胎中对芳基烃受体（AHR）激动剂的影响的抗性评估。
影响因子：
4.4
作者：
Oleksiak MF;Karchner SI;Jenny MJ;Franks DG;Welch DB;Hahn ME
通讯作者：
Hahn ME
DOI：
10.1038/nri2607
发表时间：
2009-09
期刊：
Nature reviews. Immunology
影响因子：
--
作者：
通讯作者：
--
影响因子：
4.8
作者：
Karchner, SI;Powell, WH;Hahn, ME
通讯作者：
Hahn, ME
DOI：
10.1073/pnas.93.18.9493
发表时间：
1996-09-03
影响因子：
11.1
作者：
Hochachka, PW;Buck, LT;Land, SC
通讯作者：
Land, SC
影响因子：
30.8
作者：
Oleksiak, MF;Churchill, GA;Crawford, DL
通讯作者：
Crawford, DL