Characteristics and clustering of human ribosomal protein genes

Kyota Ishii, Takanori Washio, Tamayo Uechi, Maki Yoshihama, Naoya Kenmochi, Masaru Tomita

Research output: Contribution to journalArticle

40 Citations (Scopus)

Abstract

Background: 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. Results: 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. Conclusion: 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.

Original languageEnglish
Article number37
JournalBMC Genomics
Volume7
DOIs
Publication statusPublished - 2006 Feb 28

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Ribosomal Proteins
Cluster Analysis
Genes
Codon
GA-Binding Protein Transcription Factor
Yin-Yang
Gene Expression
Amino Acids
TATA Box
Conserved Sequence
Transcription Initiation Site
Transcription Factor AP-1
Lymph Node Excision
Ribosomes
Lysine
Arginine
Mammals
Proteins
Spleen
Binding Sites

ASJC Scopus subject areas

  • Medicine(all)

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Characteristics and clustering of human ribosomal protein genes. / Ishii, Kyota; Washio, Takanori; Uechi, Tamayo; Yoshihama, Maki; Kenmochi, Naoya; Tomita, Masaru.

In: BMC Genomics, Vol. 7, 37, 28.02.2006.

Research output: Contribution to journalArticle

Ishii, Kyota ; Washio, Takanori ; Uechi, Tamayo ; Yoshihama, Maki ; Kenmochi, Naoya ; Tomita, Masaru. / Characteristics and clustering of human ribosomal protein genes. In: BMC Genomics. 2006 ; Vol. 7.
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