Tissue-specific differences in human transfer RNA expression - PubMed (original) (raw)
Comparative Study
Tissue-specific differences in human transfer RNA expression
Kimberly A Dittmar et al. PLoS Genet. 2006 Dec.
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.
Conflict of interest statement
Competing interests. The authors have declared that no competing interests exist.
Figures
Figure 1. The tRNA Microarray
(A) Schematics of fluorescence labeling of tRNA in a total RNA mixture. Ribonucleotides in the labeling oligos are shown in blue, and deoxyribonucleotides are shown in black. 5-NU, 5-allylamino-uridine; p, 5′ phosphate. All tissue samples are labeled with Cy3 and Cy5. At least two arrays are run for every sample pair. Array 1 used Cy3-labeled sample No. 1 and Cy5-labeled sample No. 2, and array 2 used Cy5-labeled sample No. 1 and Cy3-labeled sample No. 2. (B) Microarray images of one of the 32 blocks containing 100 spots hybridized with samples from HeLa (H), mouse kidney (M), and C. elegans whole animal (C). In the schematics below, black squares indicate the position of probes for the human (left), mouse (middle), and C. elegans (right) tRNAs. (C) Fluorescence intensity of a HeLa sample hybridized to the nuclear encoded tRNA probes (left) or mitochondrial encoded tRNA probes (right). “Human” indicates signals for the designated human probes; “other,” signals for Drosophila and C. elegans probes; and “mouse,” signals for mouse mitochondrial tRNA probes. (D) Dynamic range of Cy5/Cy3 ratio changes as a function of Cy3 intensity.
Figure 2. Overview of Relative tRNA Abundance among Eight Human Tissues
Red 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.
Figure 3. Comparative Expression of Nuclear and Mitochondrial Encoded tRNAs among Eight Human Tissues and Two Cell Lines Shown as TreeView Images [37]
All tissue data are normalized to the median ratio in Figure 2B and 2C. The mean and median values for the HeLa/HEK293 cell lines are 1.19 ± 0.22 and 1.20 for nuclear tRNA probes and 1.48 ± 0.37 and 1.42 for mitochondrial tRNA probes. Green indicates decreased level of expression; red, increased level of expression in the indicated tissue over brain; gray, not determined due to very low signal intensity. Data are grouped according to codon-reading abilities (isoacceptors) (A) and corresponding amino acid types (B).
Figure 4. Linear Correlation of Relative tRNA Abundance to Codon Usage of Tissue-Specific Genes that Are Expressed at High Levels
The _r_- and _p_-values are indicated in each graph. (A) Liver/brain, all data points. Excluding the two outlying data points (circled) gives a linear fit with r = 0.78, p < 0.0001, and a slope of 1.0 ± 0.2. Inclusion of these two data points gives a linear fit with r = 0.62, p = 0.00098, and a slope of 0.8 ± 0.2. (B) Three individual isoacceptors across all five tissues show linear correlation with r = 0.90 to 0.94 and p = 0.016 to 0.039. (C) Two sets of four tRNAArg isoacceptors in liver and thymus show linear correlation with r = 0.93 and 0.97 and p = 0.067 and 0.033, respectively.
Similar articles
- Post-transcriptional regulation of the steady-state levels of mitochondrial tRNAs in HeLa cells.
King MP, Attardi G. King MP, et al. J Biol Chem. 1993 May 15;268(14):10228-37. J Biol Chem. 1993. PMID: 7683672 - Deciphering tissue-specific expression profiles of mitochondrial genome-encoded tRNAs and rRNAs through transcriptomic profiling in buffalo.
Sadeesh EM, Malik A. Sadeesh EM, et al. Mol Biol Rep. 2024 Jul 31;51(1):876. doi: 10.1007/s11033-024-09815-9. Mol Biol Rep. 2024. PMID: 39083182 - Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies.
Telonis AG, Loher P, Honda S, Jing Y, Palazzo J, Kirino Y, Rigoutsos I. Telonis AG, et al. Oncotarget. 2015 Sep 22;6(28):24797-822. doi: 10.18632/oncotarget.4695. Oncotarget. 2015. PMID: 26325506 Free PMC article. - Quantifying the 'escapers' among RNA species.
Ferro I, Ignatova Z. Ferro I, et al. Biochem Soc Trans. 2015 Dec;43(6):1215-20. doi: 10.1042/BST20150158. Biochem Soc Trans. 2015. PMID: 26614663 Review. - Mitochondrial tRNA 3' end metabolism and human disease.
Levinger L, Mörl M, Florentz C. Levinger L, et al. Nucleic Acids Res. 2004 Oct 11;32(18):5430-41. doi: 10.1093/nar/gkh884. Print 2004. Nucleic Acids Res. 2004. PMID: 15477393 Free PMC article. Review.
Cited by
- Transfer RNA levels are tuned to support differentiation during Drosophila neurogenesis.
Wint R, Cleary MD. Wint R, et al. bioRxiv [Preprint]. 2024 Sep 6:2024.09.06.611608. doi: 10.1101/2024.09.06.611608. bioRxiv. 2024. PMID: 39282315 Free PMC article. Preprint. - DORQ-seq: high-throughput quantification of femtomol tRNA pools by combination of cDNA hybridization and Deep sequencing.
Kristen M, Lander M, Kilz LM, Gleue L, Jörg M, Bregeon D, Hamdane D, Marchand V, Motorin Y, Friedland K, Helm M. Kristen M, et al. Nucleic Acids Res. 2024 Oct 14;52(18):e89. doi: 10.1093/nar/gkae765. Nucleic Acids Res. 2024. PMID: 39258547 Free PMC article. - The central role of transfer RNAs in mistranslation.
Schuntermann DB, Jaskolowski M, Reynolds NM, Vargas-Rodriguez O. Schuntermann DB, et al. J Biol Chem. 2024 Sep;300(9):107679. doi: 10.1016/j.jbc.2024.107679. Epub 2024 Aug 16. J Biol Chem. 2024. PMID: 39154912 Free PMC article. Review. - Comparative analysis of 43 distinct RNA modifications by nanopore tRNA sequencing.
White LK, Dobson K, Del Pozo S, Bilodeaux JM, Andersen SE, Baldwin A, Barrington C, Körtel N, Martinez-Seidel F, Strugar SM, Watt KEN, Mukherjee N, Hesselberth JR. White LK, et al. bioRxiv [Preprint]. 2024 Jul 24:2024.07.23.604651. doi: 10.1101/2024.07.23.604651. bioRxiv. 2024. PMID: 39091754 Free PMC article. Preprint. - Impact of tRNA-induced proline-to-serine mistranslation on the transcriptome of Drosophila melanogaster.
Isaacson JR, Berg MD, Yeung W, Villén J, Brandl CJ, Moehring AJ. Isaacson JR, et al. G3 (Bethesda). 2024 Sep 4;14(9):jkae151. doi: 10.1093/g3journal/jkae151. G3 (Bethesda). 2024. PMID: 38989890 Free PMC article.
References
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources