Genomic resources for songbird research and their use in characterizing gene expression during brain development
Genomic resources for songbird research and their use in characterizing gene expression during brain development
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DOI：
10.1073/pnas.0701619104
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发表时间：
2007-04-17
影响因子：
11.1
通讯作者：
Gaasterland, Terry
中科院分区：
文献类型：
--
作者：
Li, XiaoChing;Wang, Xiu-Jie;Gaasterland, Terry
鸣禽的发声学习和神经元替代已被广泛研究，但直到最近，鸣禽研究的分子和基因组工具很少。在这里，我们描述了我们实验室开发的新分子/基因组资源。我们从斑胸草雀（Taeniopygia guttata）大脑在不同发育阶段的cDNA文库。从这些文库中随机挑选总共11，000个cDNA克隆，代表5，866个独特的基因转录物，并从3'端测序。建立了一个基于网络的数据库，用于克隆跟踪、序列分析和功能注释。我们的cDNA文库未进行标准化。未经标准化的EST测序产生了许多发育阶段特异性序列，从而深入了解了大脑发育不同阶段的基因表达模式。特别是，从孵化后第30-50天的大脑中制备的cDNA文库，对应于歌曲系统快速发育和歌曲学习的时期，具有最多样化和最丰富的基因表达。我们还鉴定了5种microRNA，它们的序列在斑胸草雀和其他物种之间高度保守。我们打印的cDNA微阵列和分析基因表达的成年雄性斑胸草雀和金丝雀（Serinus canaria）的高音中心。从基因芯片杂交结果中鉴定出在高音中心差异表达的基因。通过原位杂交验证所选择的基因。还确定了受调控基因之间的网络。这些资源为鸣禽生物学家提供了基因组注释、比较基因组学和微阵列基因表达分析的工具。
Vocal learning and neuronal replacement have been studied extensively in songbirds, but until recently, few molecular and genomic tools for songbird research existed. Here we describe new molecular/genomic resources developed in our laboratory. We made cDNA libraries from zebra finch (Taeniopygia guttata) brains at different developmental stages. A total of 11,000 cDNA clones from these libraries, representing 5,866 unique gene transcripts, were randomly picked and sequenced from the 3' ends. A web-based database was established for clone tracking, sequence analysis, and functional annotations. Our cDNA libraries were not normalized. Sequencing ESTs without normalization produced many developmental stage-specific sequences, yielding insights into patterns of gene expression at different stages of brain development. In particular, the cDNA library made from brains at posthatching day 30-50, corresponding to the period of rapid song system development and song learning, has the most diverse and richest set of genes expressed. We also identified five microRNAs whose sequences are highly conserved between zebra finch and other species. We printed cDNA microarrays and profiled gene expression in the high vocal center of both adult male zebra finches and canaries (Serinus canaria). Genes differentially expressed in the high vocal center were identified from the microarray hybridization results. Selected genes were validated by in situ hybridization. Networks among the regulated genes were also identified. These resources provide songbird biologists with tools for genome annotation, comparative genomics, and microarray gene expression analysis.