Classification and nomenclature of all human homeobox genes.
Classification and nomenclature of all human homeobox genes.
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DOI：
10.1186/1741-7007-5-47
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发表时间：
2007-10-26
期刊：
影响因子：
5.4
通讯作者：
Bruford EA
中科院分区：
文献类型：
--
作者：
Holland PW;Booth HA;Bruford EA
同源盒基因是一大类多样化的基因，其中许多在动物胚胎发育中发挥着重要作用。人们越来越多地对基因组之间的同源盒基因进行比较，试图了解动物发育的进化。尽管它们很重要，但人类同源盒基因的完整多样性此前尚未被描述过。我们已经鉴定了人类基因组常染色质区域中的所有同源盒基因和假基因，发现了许多未注释、错误注释、未命名、错误命名或错误分类的基因和假基因。我们描述了 300 个人类同源盒基因座，并将其分为 235 个可能的功能基因和 65 个可能的假基因。这些总数包括 3 个具有部分同源盒的基因和 13 个缺乏同源盒但明显源自同源盒基因的假基因。这些数字排除了重复的 DUX1 至 DUX5 同源盒序列，我们在其中鉴定了 35 个可能的假基因，预计在异染色质区域中还会有更多假基因。为大约 40 个以前未命名的基因座建立了命名法，反映了它们与人类和其他物种中其他基因座的进化关系，并提议对大约 30 个其他基因座进行命名修订。我们使用的分类可识别 11 个同源盒基因“类别”，细分为 102 个同源盒基因“家族”。我们对人类基因组中的同源盒基因和假基因进行了全面的调查，描述了许多新的位点，并修订了同源盒基因的分类和命名法。该分类方案可能广泛适用于其他动物基因组中的同源盒基因，并将促进这一重要基因超类的比较基因组学。
The homeobox genes are a large and diverse group of genes, many of which play important roles in the embryonic development of animals. Increasingly, homeobox genes are being compared between genomes in an attempt to understand the evolution of animal development. Despite their importance, the full diversity of human homeobox genes has not previously been described. We have identified all homeobox genes and pseudogenes in the euchromatic regions of the human genome, finding many unannotated, incorrectly annotated, unnamed, misnamed or misclassified genes and pseudogenes. We describe 300 human homeobox loci, which we divide into 235 probable functional genes and 65 probable pseudogenes. These totals include 3 genes with partial homeoboxes and 13 pseudogenes that lack homeoboxes but are clearly derived from homeobox genes. These figures exclude the repetitive DUX1 to DUX5 homeobox sequences of which we identified 35 probable pseudogenes, with many more expected in heterochromatic regions. Nomenclature is established for approximately 40 formerly unnamed loci, reflecting their evolutionary relationships to other loci in human and other species, and nomenclature revisions are proposed for around 30 other loci. We use a classification that recognizes 11 homeobox gene 'classes' subdivided into 102 homeobox gene 'families'. We have conducted a comprehensive survey of homeobox genes and pseudogenes in the human genome, described many new loci, and revised the classification and nomenclature of homeobox genes. The classification scheme may be widely applicable to homeobox genes in other animal genomes and will facilitate comparative genomics of this important gene superclass.
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