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Cited by 601RNA and protein synthesis mechanismsRNA modifications and cancerGenomics and Phylogenetic Studies

Tissue-Specific Differences in Human Transfer RNA Expression

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Dittmar, Kimberly A., Goodenbour, Jeffrey M., Pan, Tao·2006·PLoS Genetics
DOI 10.1371/journal.pgen.0020221PMC PMC1713254
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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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  • A human tRNA microarray has been developed for tRNA quantification and has been applied in tRNA profiling in HIV-1, specific human tissues and tumor cells, and in identifying the complete interactome of tRNA-binding proteins.

    “A human tRNA microarray has been developed for tRNA quantification and has been applied in tRNA profiling in HIV-1 (51), as well as of specific human tissues and tumor cells, and in identifying the complete interactome of tRNA-binding proteins (136 -138).”

    From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [136]

    The Introduction describes a human tRNA microarray used to compare tRNA levels in eight human tissues and two cell lines; Results/Discussion identifies HeLa among the cell lines. The paper supports the quantification and tissue/cell-line profiling portions, but our copy does not report identifying a complete interactome of tRNA-binding proteins. The HIV-1 application has a separate citation (51) and is not attributed to this source. (LLM, conf=0.86)

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Authors
Dittmar, K. A., Goodenbour, J. M., & Pan, T.
Affiliations
University of Chicago (US)
Corresponding author
Pan, Tao
ORCID
Pan, Tao
Venue
PLoS Genetics
Publisher
Public Library of Science (PLoS)
Published
2006
Volume
2
Issue
12
Pages
e221
ISSN
  • 1553-7390 (ISSN-L)
  • 1553-7404
DOI
10.1371/journal.pgen.0020221
PMC
PMC1713254
OpenAlex
W2055639102
Cited by
601
References
0
Citations by year
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FWCI
5.04
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS Genetics (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Knowledge@UChicago (University of Chicago) (submittedVersion, cc-by-nc-nd)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Figshare (submittedVersion, cc-by)
  • University of Chicago (cc-by)
Funders
  • National Science Foundation
  • University of Chicago
  • National Institutes of Health (HEK293)
  • National Institute of General Medical Sciences (T32GM007197)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
tRNA, tRNA expression, tissue-specific gene expression, fluorescent dye labeling, mitochondrial tRNA, codon usage, brain, translational regulation, human tissue
MeSH terms
RNA, Mitochondrial, Animals, Brain Chemistry, Cell Nucleus, Female, Gene Expression Regulation, HeLa Cells, Humans, Liver, Lymph Nodes, Male, Organ Specificity, RNA, RNA, Transfer, Spleen, Testis, Thymus Gland, Vulva, Oligonucleotide Array Sequence Analysis

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