Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes
Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes
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DOI：
10.1073/pnas.0337561100
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发表时间：
2003-02-04
影响因子：
11.1
通讯作者：
Brent, MR
中科院分区：
文献类型：
--
作者：
Guigó, R;Dermitzakis, ET;Brent, MR
对小鼠基因组测序的主要动机是通过使用小鼠和人类之间的序列保守性来识别编码外显子来加速哺乳动物基因的发现。事实证明，实现这一目标具有挑战性，因为小鼠和人类基因组中有很大一部分显然是保守的，但显然不编码蛋白质。我们开发了一个两阶段程序，利用小鼠和人类基因组序列产生一组基因，其实验验证率比之前报道的预测方法高得多。RT-PCR扩增和直接测序应用于小鼠预测的初始样本，这些预测不与先前已知的基因重叠，验证了139个预测中一个内含子侧翼的区域，验证率达到76%。平均而言，已证实的预测显示出比已知人类基因的小鼠直系同源物更受限制的表达模式，并且三分之二的鱼类基因组中缺乏同源物，这表明这种双基因组方法对难以找到的基因的敏感性。我们验证了已知蛋白质的112个以前未知的同源物，包括与发育生物学相关的两个同源框蛋白，一个水通道蛋白和一个肌营养不良蛋白的同源物。我们估计，转录和剪接可以验证通过这种方法确定的不重叠已知基因的> 1，000个基因预测。这很可能构成了以前未知的，多外显子哺乳动物基因的重要组成部分。
A primary motivation for sequencing the mouse genome was to accelerate the discovery of mammalian genes by using sequence conservation between mouse and human to identify coding exons. Achieving this goal proved challenging because of the large proportion of the mouse and human genomes that is apparently conserved but apparently does not code for protein. We developed a two-stage procedure that exploits the mouse and human genome sequences to produce a set of genes with a much higher rate of experimental verification than previously reported prediction methods. RT-PCR amplification and direct sequencing applied to an initial sample of mouse predictions that do not overlap previously known genes verified the regions flanking one intron in 139 predictions, with verification rates reaching 76%. On average, the confirmed predictions show more restricted expression patterns than the mouse orthologs of known human genes, and two-thirds lack homologs in fish genomes, demonstrating the sensitivity of this dual-genome approach to hard-to-find genes. We verified 112 previously unknown homologs of known proteins, including two homeobox proteins relevant to developmental biology, an aquaporin, and a homolog of dystrophin. We estimate that transcription and splicing can be verified for >1,000 gene predictions identified by this method that do not overlap known genes. This is likely to constitute a significant fraction of the previously unknown, multiexon mammalian genes.