A systematic genome-wide analysis of zebrafish protein-coding gene function.
A systematic genome-wide analysis of zebrafish protein-coding gene function.
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自人类参考基因组发表以来，与人类疾病相关的特定基因的身份正以惊人的速度被发现。一个核心问题是，这些基因的生物活性往往不清楚。在脊椎动物模式生物，通常是小鼠，详细的调查，了解这些疾病相关基因的许多直系同源物的活动是必不可少的。尽管基因靶向方法和表型分析已经导致对近6，000个蛋白质编码基因的详细了解，但这一数字与所有> 22，000个小鼠蛋白质编码基因相比明显不足福尔斯。类似地，在斑马鱼遗传学中，使用定位克隆、插入诱变、反义吗啉代寡核苷酸、靶向重测序以及锌指和TAL核酸内切酶进行的逐个基因研究对我们理解脊椎动物基因的生物活性做出了重大贡献，但再次研究的基因数量福尔斯远远低于超过26，000个斑马鱼蛋白质编码基因。重要的是，对于小鼠和斑马鱼来说，这些策略都不适合快速产生数千个基因的敲除并评估其生物活性。通过一个注释良好的斑马鱼参考基因组序列，高通量测序和有效的化学诱变，我们描述了一个积极的项目，旨在确定和表型破坏性突变的每一个斑马鱼蛋白质编码基因。到目前为止，我们已经在超过38%的已知蛋白质编码基因中发现了潜在的破坏性突变。我们已经开发了一种多等位基因表型方案，以有效地评估每个等位基因在胚胎发生过程中的影响，并分析了超过1000个等位基因的表型结果。所有的突变等位基因和数据可供社区和我们的表型分析方案是适用于胚胎发生以外的表型分析。
Since the publication of the human reference genome, the identities of specific genes associated with human diseases are being discovered at an enormous rate. A central problem is that the biological activity of these genes is often unclear. Detailed investigations in vertebrate model organisms, typically mice, have been essential for understanding the activities of many orthologues of these disease-associated genes. Although gene-targeting approaches and phenotype analysis have led to a detailed understanding of nearly 6,000 protein-coding genes, this number falls significantly short of all >22,000 mouse protein-coding genes. Similarly, in zebrafish genetics, one-by-one gene studies using positional cloning, insertional mutagenesis, antisense morpholino oligonucleotides, targeted re-sequencing and zinc finger and TAL endonucleases have made significant contributions to our understanding of the biological activity of vertebrate genes, but the number of genes studied again falls well short of the >26,000 zebrafish protein-coding genes. Importantly, for both mice and zebrafish, none of these strategies is particularly suited to the rapid generation of knockouts in thousands of genes and the assessment of their biological activity. Enabled by a well-annotated zebrafish reference genome sequence, high-throughput sequencing and efficient chemical mutagenesis, we describe an active project that aims to identify and phenotype disruptive mutations in every zebrafish protein-coding gene. Thus far we have identified potentially disruptive mutations in more than 38% of all known protein coding genes. We have developed a multi-allelic phenotyping scheme to efficiently assess the effects of each allele during embryogenesis and have analysed the phenotypic consequences of over 1000 alleles. All mutant alleles and data are available to the community and our phenotyping scheme is adaptable to phenotypic analysis beyond embryogenesis.