The Human Ribosomal Protein Genes: Sequencing and Comparative Analysis of 73 Genes

Yoshihama, Maki; Uechi, Tamayo; Asakawa, Shuichi; Kawasaki, Kazuhiko; Kato, Souichiro; Higa, Shotaro; Maeda, Noriko; Minoshima, Shinsei; Tanaka, Tatsuo; Shimizu, Nobuyoshi; Kenmochi, Naoya

doi:10.1101/gr.214202

Cited by 168 publications

(162 citation statements)

References 63 publications

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“…Based on these arguments, we counted these pseudogenic fragments as processed when we computed pseudogene density (see Table 1 footnote), but in general these fragments were treated separately from the fulllength processed pseudogene population. As the total number of these fragments is much smaller than the number of processed pseudogenes (358 vs. 2090), exclusion of them from the processed pseudogene counts does not affect the conclusions one way or another.Kenmochi and colleagues sequenced most of the 80 human RP genes and mapped them onto individual cytogenic bands (Kenmochi et al 1998;Uechi et al 2001;Yoshihama et al 2002). In our present search for processed pseudogenes, 72 of these 80 RP genes were located and their cytogenic locations were confirmed.…”

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confidence: 62%

“…Great progress has been made in recent years in elucidating the structure and mechanism of the ribosome. The peptide sequence of the complete set of mammalian RPs was deduced by Wool and colleagues (1995), and the genes encoding all human RPs have been positioned on the human genetic map (Kenmochi et al 1998;Uechi et al 2001;Yoshihama et al 2002). Moreover, several high-resolution atomic structures are now available for archaeal ribosomes (Ban et al 2000;Schluenzen et al 2000;Wimberly et al 2000;Yusupov et al 2001).…”

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confidence: 99%

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Identification and Analysis of Over 2000 Ribosomal Protein Pseudogenes in the Human Genome

Zhang¹,

Harrison²,

Gerstein³

2002

Genome Res.

187

155

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Mammals have 79 ribosomal proteins (RP). Using a systematic procedure based on sequence-homology, we have comprehensively identified pseudogenes of these proteins in the human genome. Our assignments are available at http://www.pseudogene.org or http://bioinfo.mbb.yale.edu/genome/pseudogene. In total, we found 2090 processed pseudogenes and 16 duplications of RP genes. In relation to the matching parent protein, each of the processed pseudogenes has an average relative sequence length of 97% and an average sequence identity of 76%. A small number (258) of them do not contain obvious disablements (stop codons or frameshifts) and, therefore, could be mistaken as functional genes, and 178 are disrupted by one or more repetitive elements. On average, processed pseudogenes have a longer truncation at the 5Ј end than the 3Ј end, consistent with the target-primed-reverse-transcription (TPRT) mechanism. Interestingly, on chromosome 16, an RPL26 processed pseudogene was found in the intron region of a functional RPS2 gene. The large-scale distribution of RP pseudogenes throughout the genome appears to result, chiefly, from random insertions with the numbers on each chromosome, consequently, proportional to its size. In contrast to RP genes, the RP pseudogenes have the highest density in GC-intermediate regions (41%-46%) of the genome, with the density pattern being between that of LINEs and Alus. This can be explained by a negative selection theory as we observed that GC-rich RP pseudogenes decay faster in GC-poor regions. Also, we observed a correlation between the number of processed pseudogenes and the GC content of the associated functional gene, i.e., relatively GC-poor RPs have more processed pseudogenes. This ranges from 145 pseudogenes for RPL21 down to 3 pseudogenes for RPL14. We were able to date the RP pseudogenes based on their sequence divergence from present-day RP genes, finding an age distribution similar to that for Alus. The distribution is consistent with a decline in retrotransposition activity in the hominid lineage during the last 40 Myr. We discuss the implications for retrotransposon stability and genome dynamics based on these new findings.All of the proteins in the cell are synthesized by the ribosomes, large complexes of RNA and protein molecules. A typical mammalian cell has about 4 ‫ן‬ 10 6 ribosomes, and each is composed of four RNA molecules (rRNA) and 79 ribosomal proteins (RPs). In total, ribosomes constitute about 80% of the RNA and 5%-10% of the protein in a cell (Kenmochi et al. 1998). Great progress has been made in recent years in elucidating the structure and mechanism of the ribosome. The peptide sequence of the complete set of mammalian RPs was deduced by Wool and colleagues (1995), and the genes encoding all human RPs have been positioned on the human genetic map (Kenmochi et al. 1998;Uechi et al. 2001;Yoshihama et al. 2002). Moreover, several high-resolution atomic structures are now available for archaeal ribosomes (Ban et al. 2000;Schluenzen et al. 2000;Wimberly et al. 2000;Yu...

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confidence: 62%

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confidence: 99%

Identification and Analysis of Over 2000 Ribosomal Protein Pseudogenes in the Human Genome

Zhang¹,

Harrison²,

Gerstein³

2002

Genome Res.

187

155

View full text Add to dashboard Cite

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“…Genes encoding ribosomal proteins (RPs) may be highly suitable for designing universal primers, as RPs are the most highly conserved genes among eukaryotes and are typically encoded by a single gene (Wool 1979;Wool et al 1995). Indeed, the coding sequences of RP genes are reported to be highly conserved among humans, fruit flies, and nematodes (Yoshihama et al 2002). In this study, we designed 19 primer pairs in exons of 12 RP genes and demonstrated the universal utility of these primer pairs using samples of distantly related aquatic animal species.…”

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confidence: 99%

Universal primers for exon-priming intron-crossing (EPIC) PCR on ribosomal protein genes in marine animals

Chow

Yanagimoto

Nakamura³

2015

Int Aquat Res

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Relatively conserved exon sequences among distant aquatic animal taxa (Copepoda, Echinodermata, and Teleostei) were determined for 12 ribosomal protein genes, and 19 primer pairs were designed for an exon-primed intron-crossing polymerase chain reaction strategy. The universal utility of these primers was evaluated in distant animal species (sea urchin, squid, crab, shark, and tuna). Fragment amplification was confirmed for at least three species for all primer pairs, and single fragment amplification was observed for at least one species in 16 primer pairs. Primer sets presented here may serve as an initial step for isolating singlecopy nuclear DNA sequences in a wide variety of marine animals.

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“…It maps at the chromosomal locus 18q21 and codes for the 60S subunit and belongs to the L22P family of ribosomal proteins. 49 It functions in RNA-binding, signal transduction of the NFjB pathway and structural constituency of the ribosome. 50 The clone 1.1 finds identity to the human ribosomal RPL27A gene encoding the ribosomal protein L27a harboring the large 60S subunit.…”

Section: Insert-comparison With Genomic Databasesmentioning

confidence: 99%

Induced and repressed genes after irradiation sensitizing by pentoxyphylline

Waldeck

Strunz

Müller

et al. 2006

Intl Journal of Cancer

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Aim in cancer therapy is to increase the therapeutic ratio eliminating the disease while minimizing toxicity to normal tissues. Radiation therapy is a main component in targeting cancer. Radiosensitizing agents like pentoxyphylline (PTX) have been evaluated to improve radiotherapy. Commonly, cells respond to radiation by the activation of specific early and late response genes as well as by inhibition of genes, which are expressed under normal conditions. A display of the genetic distinctions at the level of transcription is given here to characterize the molecular events underlying the radiosensitizing mechanisms. The method of suppression subtractive hybridization allows the visualization of both induced and repressed genes in irradiated cells compared with cells sensitized immediately after irradiation. The genes were isolated by cDNA-cloning, differential analysis and sequence similarity search. Genes involved in protein synthesis, metabolism, proteolysis and transcriptional regulation were detected. It is important that genes like KIAA280, which were only known as unidentified EST sequences before without function, but inaccessible by array technology were recovered as functional genes. Database searches for PTX-induced genes detected a human mRNA completely unknown. In case of suppressed genes, we detected several mRNAs; one thereof shows homology to a hypothetical protein possibly involved in signal transduction. A further mRNA encodes the protein BM036 supposed to associate with the E2F transcription factor. A hypothetical protein H41 was detected, which may repress the Her-2/neu receptor influencing breast cancer, gliomas and prostate tumors. Radiation combined with PTX may lead to a better prognosis by down regulation of the Her-2/neu, which will be proven by clinical studies in the near future. The connection between cancerogenesis and cyclins has been demonstrated with the aberrant expression of members of the family of cyclins and the mechanisms of the cell cycle G1 arrest and apoptosis were well documented. [3][4][5][6][7] The mechanisms of G2 arrest in contrast have been described to a lesser extent, although this event could be of relevance to the cellular survival after photonirradiation. 8,9 Beyond doubt, the G2-phase arrest is generally activated in response to DNA damage independent of the p53 status. 8 It acts as an universal feedback for maintaining the genomic integrity and for survival after irradiation by repairing DNA breaks prior to mitosis. 10 Much of the underlying knowledge on the G2/M phase was obtained by studying genes involved in the regulation of DNA damage response because DNA-damaging processes, like g-radiation, respond by arresting at cell cycle checkpoints. 11 This ''G2 delay'' after photon-irradiation involves molecular mechanisms like reduced cyclin B levels and inhibition of the Cdk1 activity. 8 Formation and activation of the maturation promoting factor (MPF) are pivotal for the G2/M checkpoint regulation. The transition from G2 into the mitosis occurs by the activatio...

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The Human Ribosomal Protein Genes: Sequencing and Comparative Analysis of 73 Genes

Cited by 168 publications

References 63 publications

Identification and Analysis of Over 2000 Ribosomal Protein Pseudogenes in the Human Genome

Identification and Analysis of Over 2000 Ribosomal Protein Pseudogenes in the Human Genome

Universal primers for exon-priming intron-crossing (EPIC) PCR on ribosomal protein genes in marine animals

Induced and repressed genes after irradiation sensitizing by pentoxyphylline

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