牛SOCS5基因5′调控区多态性研究

Polymorphisms of 5'-flanking region of SOCS5 gene in cattle

【目的】筛选SOCS5基因启动子区多态位点(SNP),并研究其对启动子功能元件的影响。【方法】选择贵州地方优良品种务川黑牛和中国荷斯坦奶牛两种生长性能差异明显的品种构建DNA池,直接测序后用DNASTAR软件进行序列拼接和校正,BLAST分析SOCS5基因多态性,然后用生物信息学软件预测序列核心启动子区和CpG岛,分析SNP位点对转录因子结合位点影响。【结果】牛SOCS5基因5'调控区和第1外显子区存在3个SNP位点,分别为:C-577T、T-43C和C+61T,其中C+61T与SNP数据库中的rs110977810信息相符,C-577T和T-43C为新发现SNP位点。生物信息学软件预测得到SOCS5基因核心启动子区和CpG岛,SNP位点导致附近大量转录因子结合位点消失和新位点产生;SNP位点对转录因子结合位点有显著影响,但对核心启动子范围和起始位点无明显影响,不在甲基化水平上影响SOCS5基因表达水平。【结论】牛SOCS5基因5'调控区存在3个对启动子功能元件有较大影响的SNP位点。

[ Objective ]SNP sites in the promoter region of SOCS5 gene in cattle were screened in order to analyze the effect of SNPs on function elements of promoter. [Method]Two cattle breeds （Wuchuan black cattle and Chinese Holstein cow） possessing significant difference in growth performance were selected to construct DNA pools. After direct sequencing, sequence jointing and adjusting were conducted using DNASTAR software. The polymorphisms of SOCS5 gene was analyzed using BLAST. Sequence core promoter region and CpG island were predicted using bioinformatics software. Finally the effects of SNP site on transcription factor binding sites were assayed. [Result ]Three SNPs including C-577T, T- 43C and C＋61T were found in the 5′ flanking region and exon 1 of SOCS5 gene. The C＋61T accorded with rs110977810 in SNP database, while C-577T and T-43C were newly found sites. Furthermore, bioinformatics tools were used to predict the core region of promoter and CpG island. It was demonstrated that various novel transcription factors binding sites emerged while a large amount of transcription factors binding sites disappeared. SNP mutation could change transcription factors binding sites but it did not affect the range or initiation site of promoter dramatically, which meant that SNP had no effect on SOCS5 gene expression at the methylation level. [Conclusion]There were three SNPs existing in the 5′ flanking region of SOCS5 gene that had important effects on promoter elements.