Transcriptome analysis of zebrafish embryogenesis using microarrays.
Transcriptome analysis of zebrafish embryogenesis using microarrays.
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DOI：
10.1371/journal.pgen.0010029
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发表时间：
2005-08
期刊：
影响因子：
4.5
通讯作者：
Lufkin T
中科院分区：
文献类型：
--
作者：
Mathavan S;Lee SG;Mak A;Miller LD;Murthy KR;Govindarajan KR;Tong Y;Wu YL;Lam SH;Yang H;Ruan Y;Korzh V;Gong Z;Liu ET;Lufkin T
斑马鱼（Danio rerio）是脊椎动物发育遗传学研究的公认模型，但同时对斑马鱼胚胎发生的转录事件知之甚少。在这里，我们采用微阵列分析研究斑马鱼胚胎发育过程中的发育调控基因的时间活动。转录组分析在12个不同的胚胎时间点，涵盖5个不同的发育阶段（母体，囊胚，原肠胚，分割，和咽）揭示了一个高度动态的转录谱。层次聚类，阶段特异性聚类和算法来检测基因表达的起始和峰值，揭示了在不同发育阶段具有最大基因活性的清晰分界的转录本簇以及参与专门功能如器官发生的基因组的共调节表达。我们的研究还揭示了一个先前未识别的基因组，这些基因在囊胚中期过渡之前转录，这一时间点早于传统上认为合子基因组变得活跃的时间点。在这里，我们提供了，第一次我们的知识，发育调控斑马鱼基因及其在胚胎发育过程中的表达谱，包括新的信息的时间表达的几千个以前未知的基因的全面列表。本研究产生的表达数据可供所有感兴趣的科学家从我们的研究所资源数据库（http：//giscompute.gis.a-star.edu.sg/zebrafish/data_download.html）访问。为了揭示胚胎发生的神秘分子过程，科学家们采用了高密度微阵列的强大技术方法，首次分析了（据我们所知）超过16，000个斑马鱼基因在胚胎发育主要阶段的表达模式。他们确定，斑马鱼中发育调控基因可以根据转录积累开始（激活）的时间和活性峰值（峰值积累）进行分组。例如，编码转录调节因子的基因比它们控制的靶基因更早地被激活。因此，斑马鱼的发育基因表达谱可以分为连续波的基因激活，然后是峰值活性。在这项研究中发现的一组非常新颖的基因是一组大约100个基因，它们的激活时间甚至比以前认为的胚胎转录激活的最早时间还要早。这些基因可能对准备胚胎细胞进行后续高水平基因组激活和正常发育很重要。
Zebrafish (Danio rerio) is a well-recognized model for the study of vertebrate developmental genetics, yet at the same time little is known about the transcriptional events that underlie zebrafish embryogenesis. Here we have employed microarray analysis to study the temporal activity of developmentally regulated genes during zebrafish embryogenesis. Transcriptome analysis at 12 different embryonic time points covering five different developmental stages (maternal, blastula, gastrula, segmentation, and pharyngula) revealed a highly dynamic transcriptional profile. Hierarchical clustering, stage-specific clustering, and algorithms to detect onset and peak of gene expression revealed clearly demarcated transcript clusters with maximum gene activity at distinct developmental stages as well as co-regulated expression of gene groups involved in dedicated functions such as organogenesis. Our study also revealed a previously unidentified cohort of genes that are transcribed prior to the mid-blastula transition, a time point earlier than when the zygotic genome was traditionally thought to become active. Here we provide, for the first time to our knowledge, a comprehensive list of developmentally regulated zebrafish genes and their expression profiles during embryogenesis, including novel information on the temporal expression of several thousand previously uncharacterized genes. The expression data generated from this study are accessible to all interested scientists from our institute resource database (http://giscompute.gis.a-star.edu.sg/~govind/zebrafish/data_download.html). In an effort to shed light on the mysterious molecular process of embryogenesis, scientists have employed the powerful technological approach of high-density microarrays to analyze for the first time (to our knowledge) the expression patterns of over 16,000 zebrafish genes during the major stages of embryonic development. They determined that developmentally regulated genes in zebrafish could be grouped based upon their time of transcript accumulation onset (activation) and their peak of activity (peak accumulation). For example, genes encoding transcriptional regulators are activated en masse earlier than the target genes that they control. Thus, the developmental gene expression profile in zebrafish can be grouped into successive waves of gene activation followed by peak activity. One very novel group of genes that was discovered in this study is a set of about 100 genes that are activated even earlier than what was previously thought to be the earliest time of embryonic transcriptional activation. These genes are likely to be important for preparing the embryonic cells for subsequent high-level genome activation and normal development.
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