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.
Highlights
Human tissues contain common and distinct macromolecular components in varying amounts
There are approximately 473 human Transfer RNA (tRNA) that are grouped into 49 isoacceptor families to decode the 21 amino acids specified by the genetic code (20 standard amino acids and selenocysteine)
Our results show that tRNA levels vary widely among human tissues and coordinate according to the properties of their cognate amino acids
Summary
Human tissues contain common and distinct macromolecular components in varying amounts. The relative expression of nuclear encoded tRNAs in two commonly used cell lines (HeLa and HEK293) differs by less than twofold and is quite similar among the isoacceptors (Figures 3 and S1 and Table 1) This result suggests that tRNA isoacceptor levels do not play a major role in differential protein expression in these cell lines, even though they are derived from different tissues (cervix and embryonic kidney). Correlations of the abundance of tRNA isoacceptors to codon usage are derived primarily from genes that are translated at high levels (e.g., ribosomal proteins) Adapting this strategy, thresholds were algorithmically established to determine the top 13 to 43 tissue-specific transcripts according to the Human GeneAtlas GNF1H gcRMA dataset at http://symatlas.gnf.org/SymAtlas [2].
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