Liu Wu-Yi, Zhao Chun-Jiang
Department of Animal Science, China Agricultural University, Yuanmingyuan West Road No.2, Beijing 100093, China.
Comp Funct Genomics. 2010;2010:682095. doi: 10.1155/2010/682095. Epub 2010 May 3.
Members of the basic helix-loop-helix (bHLH) family of transcription factors play important roles in a wide range of developmental processes. In this study, we conducted a genome-wide survey using the chicken (Gallus gallus) genomic database, and identified 104 bHLH sequences belonging to 42 gene families in an effort to characterize the chicken bHLH transcription factor family. Phylogenetic analyses revealed that chicken has 50, 21, 15, 4, 8, and 3 bHLH members in groups A, B, C, D, E, and F, respectively, while three members belonging to none of these groups were classified as ''orphans". A comparison between chicken and human bHLH repertoires suggested that both organisms have a number of lineage-specific bHLH members in the proteomes. Chromosome distribution patterns and phylogenetic analyses strongly suggest that the bHLH members should have arisen through gene duplication at an early date. Gene Ontology (GO) enrichment statistics showed 51 top GO annotations of biological processes counted in the frequency. The present study deepens our understanding of the chicken bHLH transcription factor family and provides much useful information for further studies using chicken as a model system.
基本螺旋-环-螺旋(bHLH)转录因子家族成员在广泛的发育过程中发挥着重要作用。在本研究中,我们利用鸡(Gallus gallus)基因组数据库进行了全基因组调查,鉴定出属于42个基因家族的104个bHLH序列,旨在对鸡bHLH转录因子家族进行特征描述。系统发育分析表明,鸡在A、B、C、D、E和F组中分别有50、21、15、4、8和3个bHLH成员,而不属于这些组的三个成员被归类为“孤儿”。鸡与人bHLH蛋白质组的比较表明,这两种生物在蛋白质组中都有许多谱系特异性的bHLH成员。染色体分布模式和系统发育分析强烈表明,bHLH成员应该在早期通过基因复制产生。基因本体论(GO)富集统计显示,按频率计算有51个顶级生物过程GO注释。本研究加深了我们对鸡bHLH转录因子家族的理解,并为以鸡为模型系统的进一步研究提供了许多有用信息。