| 引用本文: | 王樟凤,卓亮亮,黄子琦,柴学文,饶友生.鸡基因组差异表达基因翻译起始密码子上下游序列的比较研究[J].生物信息学,2014,12(4):. |
| WANG Zhangfeng,ZHUO Liangliang,HUANG Ziqi,CHAI Xuewen,RAO Yousheng.Comparison of the sequences around the translation initiation codon between differentially expressed genes in chicken[J].Chinese Journal of Bioinformatics,2014,12(4):. |
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| 摘要: |
| 翻译起始调控是基因表达调控的一个关键步骤之一。本文以鸡为研究材料,比较研究了鸡基因组高表达基因和低表达基因翻译起始密码子上下游的碱基序列差异,旨在寻找影响鸡基因表达水平的特异性调控位点。全部3020个单剪接基因完整的mRNA序列及有详细注释的5′UTRs序列从Ensembl下载。编写计算机程序,读取每个基因mRNA起始密码子上下游各位点的碱基。研究发现,起始密码子上游-3、-2位点可能是鸡基因组基因表达起始密码子正确识别的关键位点。起始密码子上下游的碱基组成分析发现,高表达基因和低表达基因起始密码子的上游均倾向使用( G+C),高表达基因的使用偏倚尤为强烈。序列差异比较发现,高表达基因在-9、-6、-3、+4位点显著偏向G,在-1、-2、-4、-5位点显著偏向C。低表达基因起始密码子上游使用A、U的频率显著高于低表达基因。在-19位点强烈偏向A,在+1、+11、+14位点强烈偏向U。 |
| 关键词: 鸡 基因表达调控 起始密码子 序列差异 |
| DOI：10.3969/j.issn.1672-5565.2014-04.20140405 |
| 分类号: |
| 基金项目:江西省教育厅科学技术研究项目( GJJ 13781, GJJ14781)。 |
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| Comparison of the sequences around the translation initiation codon between differentially expressed genes in chicken |
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WANG Zhangfeng, ZHUO Liangliang, HUANG Ziqi, CHAI Xuewen, RAO Yousheng
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Department of Biological Technology, Nanchang Normal University, Nanchang Jiangxi 330046,China
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| Abstract: |
| The control of translation initiation is one of the most fundamental processes in the regulation of gene expression. Here, we investigated the differences of the sequences around the translation initiation codon between highly and lowly expressed genes, and searched for the specific sites regulating gene expression in chicken. Total 3 020 nuclear genes with complete CDSs and no evidence of multiple-splicing forms were included in this study. The complete mRNA sequences and 5′ UTRs sequences corresponding to all annotated genes in chicken were downloaded from Ensembl. Sequences around translation initiation codon of the genes were extracted by a personal program. We found that the -3 and -2 sites, upstream of the initiation codon, are more likely the key sites for correct recognition of the translation initiation codon in the chicken genome. Analyses of base composition around the initiation codons indicated that the upstream of the initiation codons tends to use G+C, especially for highly expressed genes. We also found strong bias of G at position -9,-6,-3 and+4 and strong bias of C at position-1,-2,-4 and-5 in the highly expressed genes. The A and U occurrence frequency of upstream of the initiation codon in the lowly expressed genes is significantly high than that in the highly expressed genes. A strong bias of A was found at position-19, and another strong bias of U was found at position +1, +11, and 14 in the lowly expressed genes. We argued that these sites are more likely the important regulation sites of gene expression, and deserve more further attention. |
| Key words: Chicken Gene expression Regulation initiation codon Sequence difference |
