Characteristics and clustering of human ribosomal protein genes.
Characteristics and clustering of human ribosomal protein genes.
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DOI：
10.1186/1471-2164-7-37
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发表时间：
2006-02-28
期刊：
影响因子：
4.4
通讯作者：
Tomita M
中科院分区：
文献类型：
--
作者：
Ishii K;Washio T;Uechi T;Yoshihama M;Kenmochi N;Tomita M
核糖体是翻译系统的中心参与者，在哺乳动物中，翻译系统由四个RNA物种和79个核糖体蛋白(RP)组成。基因表达的调控机制和RPS的功能被认为是相同的。大多数RP基因都有共同的启动子，因此被认为具有统一的基因表达调控机制。我们从表达谱、启动子结构、编码的氨基酸组成和密码子组成等方面系统地分析了RP基因的同质性和异质性。结果表明：(1)大多数RP基因在mRNA水平上协同表达，在脾、淋巴清扫(LND)和胎脑中的信号较高。然而，包括P蛋白基因(RPLP0、RPLP1、RPLP2)在内的17个基因以组织特异性的方式表达。(2)大多数启动子都有GC盒和核呼吸因子2、阴阳1和/或激活蛋白1的可能结合部位，但它们没有典型的TATA盒。(3)氨基酸组成分析表明，编码蛋白中含有较高的赖氨酸和精氨酸。(4)主要RP基因具有同义密码子结构特征，第三密码子G或C率较高，AAG、CAG、ATC、GAG、CAC和CTG含量较高。其中11个RP基因仍被鉴定为独特的，并且至少没有表现出上述特征中的一部分，这表明它们可能具有其他RP基因中不存在的未知功能。此外，我们发现在转录起始点附近和内含子区域，人和小鼠基因之间的序列是保守的。这项研究提示了人类RP基因的某些总体趋势和特征。
The ribosome is a central player in the translation system, which in mammals consists of four RNA species and 79 ribosomal proteins (RPs). The control mechanisms of gene expression and the functions of RPs are believed to be identical. Most RP genes have common promoters and were therefore assumed to have a unified gene expression control mechanism. We systematically analyzed the homogeneity and heterogeneity of RP genes on the basis of their expression profiles, promoter structures, encoded amino acid compositions, and codon compositions. The results revealed that (1) most RP genes are coordinately expressed at the mRNA level, with higher signals in the spleen, lymph node dissection (LND), and fetal brain. However, 17 genes, including the P protein genes (RPLP0, RPLP1, RPLP2), are expressed in a tissue-specific manner. (2) Most promoters have GC boxes and possible binding sites for nuclear respiratory factor 2, Yin and Yang 1, and/or activator protein 1. However, they do not have canonical TATA boxes. (3) Analysis of the amino acid composition of the encoded proteins indicated a high lysine and arginine content. (4) The major RP genes exhibit a characteristic synonymous codon composition with high rates of G or C in the third-codon position and a high content of AAG, CAG, ATC, GAG, CAC, and CTG. Eleven of the RP genes are still identified as being unique and did not exhibit at least some of the above characteristics, indicating that they may have unknown functions not present in other RP genes. Furthermore, we found sequences conserved between human and mouse genes around the transcription start sites and in the intronic regions. This study suggests certain overall trends and characteristic features of human RP genes.
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