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Tissue-specific differences in human transfer RNA expression.

Dittmar KA, Goodenbour JM, Pan T - PLoS Genet. (2006)

Bottom Line: We found tissue-specific differences in the expression of individual tRNA species, and tRNAs decoding amino acids with similar chemical properties exhibited coordinated expression in distinct tissue types.Relative tRNA abundance exhibits a statistically significant correlation to the codon usage of a collection of highly expressed, tissue-specific genes in a subset of tissues or tRNA isoacceptors.Our findings demonstrate the existence of tissue-specific expression of tRNA species that strongly implicates a role for tRNA heterogeneity in regulating translation and possibly additional processes in vertebrate organisms.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America.

ABSTRACT
Over 450 transfer RNA (tRNA) genes have been annotated in the human genome. Reliable quantitation of tRNA levels in human samples using microarray methods presents a technical challenge. We have developed a microarray method to quantify tRNAs based on a fluorescent dye-labeling technique. The first-generation tRNA microarray consists of 42 probes for nuclear encoded tRNAs and 21 probes for mitochondrial encoded tRNAs. These probes cover tRNAs for all 20 amino acids and 11 isoacceptor families. Using this array, we report that the amounts of tRNA within the total cellular RNA vary widely among eight different human tissues. The brain expresses higher overall levels of nuclear encoded tRNAs than every tissue examined but one and higher levels of mitochondrial encoded tRNAs than every tissue examined. We found tissue-specific differences in the expression of individual tRNA species, and tRNAs decoding amino acids with similar chemical properties exhibited coordinated expression in distinct tissue types. Relative tRNA abundance exhibits a statistically significant correlation to the codon usage of a collection of highly expressed, tissue-specific genes in a subset of tissues or tRNA isoacceptors. Our findings demonstrate the existence of tissue-specific expression of tRNA species that strongly implicates a role for tRNA heterogeneity in regulating translation and possibly additional processes in vertebrate organisms.

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Overview of Relative tRNA Abundance among Eight Human TissuesRed line indicates the same level as brain.(A) Relative ratios of each human tRNA probe for ovary or spleen versus brain sorted according to the ratios for ovary. Left, nuclear encoded tRNAs; right, mitochondrial encoded tRNAs.(B) Mean and median values of the nuclear tRNA probes for seven tissues versus brain.(C) Mean and median values of the mitochondrial tRNA probes.
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pgen-0020221-g002: Overview of Relative tRNA Abundance among Eight Human TissuesRed line indicates the same level as brain.(A) Relative ratios of each human tRNA probe for ovary or spleen versus brain sorted according to the ratios for ovary. Left, nuclear encoded tRNAs; right, mitochondrial encoded tRNAs.(B) Mean and median values of the nuclear tRNA probes for seven tissues versus brain.(C) Mean and median values of the mitochondrial tRNA probes.

Mentions: Microarray results show overall variations in the expression levels of tRNA among different tissues (Figures 2 and S1). For example, all tRNAs in ovary have lower levels relative to brain. Some tRNAs in spleen have higher, while others have lower levels, compared to those in brain (Figure 2A). Within individual tissues, the maximal differences between the relative tRNA levels can be as large as approximately tenfold (e.g., vulva, thymus) or only approximately threefold (e.g., testis).


Tissue-specific differences in human transfer RNA expression.

Dittmar KA, Goodenbour JM, Pan T - PLoS Genet. (2006)

Overview of Relative tRNA Abundance among Eight Human TissuesRed line indicates the same level as brain.(A) Relative ratios of each human tRNA probe for ovary or spleen versus brain sorted according to the ratios for ovary. Left, nuclear encoded tRNAs; right, mitochondrial encoded tRNAs.(B) Mean and median values of the nuclear tRNA probes for seven tissues versus brain.(C) Mean and median values of the mitochondrial tRNA probes.
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Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1713254&req=5

pgen-0020221-g002: Overview of Relative tRNA Abundance among Eight Human TissuesRed line indicates the same level as brain.(A) Relative ratios of each human tRNA probe for ovary or spleen versus brain sorted according to the ratios for ovary. Left, nuclear encoded tRNAs; right, mitochondrial encoded tRNAs.(B) Mean and median values of the nuclear tRNA probes for seven tissues versus brain.(C) Mean and median values of the mitochondrial tRNA probes.
Mentions: Microarray results show overall variations in the expression levels of tRNA among different tissues (Figures 2 and S1). For example, all tRNAs in ovary have lower levels relative to brain. Some tRNAs in spleen have higher, while others have lower levels, compared to those in brain (Figure 2A). Within individual tissues, the maximal differences between the relative tRNA levels can be as large as approximately tenfold (e.g., vulva, thymus) or only approximately threefold (e.g., testis).

Bottom Line: We found tissue-specific differences in the expression of individual tRNA species, and tRNAs decoding amino acids with similar chemical properties exhibited coordinated expression in distinct tissue types.Relative tRNA abundance exhibits a statistically significant correlation to the codon usage of a collection of highly expressed, tissue-specific genes in a subset of tissues or tRNA isoacceptors.Our findings demonstrate the existence of tissue-specific expression of tRNA species that strongly implicates a role for tRNA heterogeneity in regulating translation and possibly additional processes in vertebrate organisms.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America.

ABSTRACT
Over 450 transfer RNA (tRNA) genes have been annotated in the human genome. Reliable quantitation of tRNA levels in human samples using microarray methods presents a technical challenge. We have developed a microarray method to quantify tRNAs based on a fluorescent dye-labeling technique. The first-generation tRNA microarray consists of 42 probes for nuclear encoded tRNAs and 21 probes for mitochondrial encoded tRNAs. These probes cover tRNAs for all 20 amino acids and 11 isoacceptor families. Using this array, we report that the amounts of tRNA within the total cellular RNA vary widely among eight different human tissues. The brain expresses higher overall levels of nuclear encoded tRNAs than every tissue examined but one and higher levels of mitochondrial encoded tRNAs than every tissue examined. We found tissue-specific differences in the expression of individual tRNA species, and tRNAs decoding amino acids with similar chemical properties exhibited coordinated expression in distinct tissue types. Relative tRNA abundance exhibits a statistically significant correlation to the codon usage of a collection of highly expressed, tissue-specific genes in a subset of tissues or tRNA isoacceptors. Our findings demonstrate the existence of tissue-specific expression of tRNA species that strongly implicates a role for tRNA heterogeneity in regulating translation and possibly additional processes in vertebrate organisms.

Show MeSH