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Ward C, Beharry A, Tennakoon R, Rozik P, Wilhelm SDP, Heinemann IU, O'Donoghue P. Mechanisms and Delivery of tRNA Therapeutics. Chem Rev 2024. [PMID: 38801719 DOI: 10.1021/acs.chemrev.4c00142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Transfer ribonucleic acid (tRNA) therapeutics will provide personalized and mutation specific medicines to treat human genetic diseases for which no cures currently exist. The tRNAs are a family of adaptor molecules that interpret the nucleic acid sequences in our genes into the amino acid sequences of proteins that dictate cell function. Humans encode more than 600 tRNA genes. Interestingly, even healthy individuals contain some mutant tRNAs that make mistakes. Missense suppressor tRNAs insert the wrong amino acid in proteins, and nonsense suppressor tRNAs read through premature stop signals to generate full length proteins. Mutations that underlie many human diseases, including neurodegenerative diseases, cancers, and diverse rare genetic disorders, result from missense or nonsense mutations. Thus, specific tRNA variants can be strategically deployed as therapeutic agents to correct genetic defects. We review the mechanisms of tRNA therapeutic activity, the nature of the therapeutic window for nonsense and missense suppression as well as wild-type tRNA supplementation. We discuss the challenges and promises of delivering tRNAs as synthetic RNAs or as gene therapies. Together, tRNA medicines will provide novel treatments for common and rare genetic diseases in humans.
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Bell CG. Epigenomic insights into common human disease pathology. Cell Mol Life Sci 2024; 81:178. [PMID: 38602535 PMCID: PMC11008083 DOI: 10.1007/s00018-024-05206-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
The epigenome-the chemical modifications and chromatin-related packaging of the genome-enables the same genetic template to be activated or repressed in different cellular settings. This multi-layered mechanism facilitates cell-type specific function by setting the local sequence and 3D interactive activity level. Gene transcription is further modulated through the interplay with transcription factors and co-regulators. The human body requires this epigenomic apparatus to be precisely installed throughout development and then adequately maintained during the lifespan. The causal role of the epigenome in human pathology, beyond imprinting disorders and specific tumour suppressor genes, was further brought into the spotlight by large-scale sequencing projects identifying that mutations in epigenomic machinery genes could be critical drivers in both cancer and developmental disorders. Abrogation of this cellular mechanism is providing new molecular insights into pathogenesis. However, deciphering the full breadth and implications of these epigenomic changes remains challenging. Knowledge is accruing regarding disease mechanisms and clinical biomarkers, through pathogenically relevant and surrogate tissue analyses, respectively. Advances include consortia generated cell-type specific reference epigenomes, high-throughput DNA methylome association studies, as well as insights into ageing-related diseases from biological 'clocks' constructed by machine learning algorithms. Also, 3rd-generation sequencing is beginning to disentangle the complexity of genetic and DNA modification haplotypes. Cell-free DNA methylation as a cancer biomarker has clear clinical utility and further potential to assess organ damage across many disorders. Finally, molecular understanding of disease aetiology brings with it the opportunity for exact therapeutic alteration of the epigenome through CRISPR-activation or inhibition.
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Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts & The London Faculty of Medicine, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
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Wu Z, Zhang W, Qu J, Liu GH. Emerging epigenetic insights into aging mechanisms and interventions. Trends Pharmacol Sci 2024; 45:157-172. [PMID: 38216430 DOI: 10.1016/j.tips.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Epigenetic dysregulation emerges as a critical hallmark and driving force of aging. Although still an evolving field with much to explore, it has rapidly gained significance by providing valuable insights into the mechanisms of aging and potential therapeutic opportunities for age-related diseases. Recent years have witnessed remarkable strides in our understanding of the epigenetic landscape of aging, encompassing pivotal elements, such as DNA methylation, histone modifications, RNA modifications, and noncoding (nc) RNAs. Here, we review the latest discoveries that shed light on new epigenetic mechanisms and critical targets for predicting and intervening in aging and related disorders. Furthermore, we explore burgeoning interventions and exemplary clinical trials explicitly designed to foster healthy aging, while contemplating the potential ramifications of epigenetic influences.
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Affiliation(s)
- Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Weiqi Zhang
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jing Qu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
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Fonseca PAS, Suárez-Vega A, Esteban-Blanco C, Pelayo R, Marina H, Gutiérrez-Gil B, Arranz JJ. Epigenetic regulation of functional candidate genes for milk production traits in dairy sheep subjected to protein restriction in the prepubertal stage. BMC Genomics 2023; 24:511. [PMID: 37658326 PMCID: PMC10472666 DOI: 10.1186/s12864-023-09611-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/21/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND As the prepubertal stage is a crucial point for the proper development of the mammary gland and milk production, this study aims to evaluate how protein restriction at this stage can affect methylation marks in milk somatic cells. Here, 28 Assaf ewes were subjected to 42.3% nutritional protein restriction (14 animals, NPR) or fed standard diets (14 animals, C) during the prepubertal stage. During the second lactation, the milk somatic cells of these ewes were sampled, and the extracted DNA was subjected to whole-genome bisulfite sequencing. RESULTS A total of 1154 differentially methylated regions (DMRs) were identified between the NPR and C groups. Indeed, the results of functional enrichment analyses of the genes harboring these DMRs suggested their relevant effects on the development of the mammary gland and lipid metabolism in sheep. The additional analysis of the correlations of the mean methylation levels within these DMRs with fat, protein, and dry extract percentages in the milk and milk somatic cell counts suggested associations between several DMRs and milk production traits. However, there were no phenotypic differences in these traits between the NPR and C groups. CONCLUSION In light of the above, the results obtained in the current study might suggest potential candidate genes for the regulation of milk production traits in the sheep mammary gland. Further studies focusing on elucidating the genetic mechanisms affected by the identified DMRs may help to better understand the biological mechanisms modified in the mammary gland of dairy sheep as a response to nutritional challenges and their potential effects on milk production.
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Affiliation(s)
- P. A. S. Fonseca
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071 León, Spain
| | - A. Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071 León, Spain
| | - C. Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071 León, Spain
| | - R. Pelayo
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071 León, Spain
| | - H. Marina
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071 León, Spain
| | - B. Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071 León, Spain
| | - J. J. Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071 León, Spain
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Cross T, Haug KBF, Brusletto BS, Ommundsen SK, Trøseid AMS, Aspelin T, Olstad OK, Aass HCD, Galtung HK, Utheim TP, Jensen JL, Øvstebø R. Non-Coding RNA in Salivary Extracellular Vesicles: A New Frontier in Sjögren's Syndrome Diagnostics? Int J Mol Sci 2023; 24:13409. [PMID: 37686214 PMCID: PMC10488010 DOI: 10.3390/ijms241713409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Sjögren's syndrome is an autoimmune rheumatic disease characterized by inflammation of the salivary and lacrimal glands, often manifesting as dry mouth and dry eyes. To simplify diagnostics of primary Sjögren's syndrome (pSS), a non-invasive marker is needed. The aim of the study was to compare the RNA content of salivary extracellular vesicles (EVs) between patients with pSS and healthy controls using microarray technology. Stimulated whole saliva was collected from 11 pSS patients and 11 age-matched controls. EV-RNA was isolated from the saliva samples using a Qiagen exoRNeasy Midi Kit and analyzed using Affymetrix Clariom D™ microarrays. A one-way ANOVA test was used to compare the mean signal values of each transcript between the two groups. A total of 9307 transcripts, coding and non-coding RNA, were detected in all samples. Of these transcripts, 1475 showed statistically significant differential abundance between the pSS and the control groups, generating two distinct EV-RNA patterns. In particular, tRNAs were downregulated in pSS patients, with the transcript tRNA-Ile-AAT-2-1 showing a 2-fold difference, and a promise as a potential biomarker candidate. This study therein demonstrates the potential for using salivary EV-RNA in pSS diagnostics.
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Affiliation(s)
- Tanya Cross
- The Regenerative Medicine Unit, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | - Kari Bente Foss Haug
- The Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | - Berit Sletbakk Brusletto
- The Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | - Stine Kamilla Ommundsen
- The Regenerative Medicine Unit, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | - Anne-Marie Siebke Trøseid
- The Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | - Trude Aspelin
- The Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | - Ole Kristoffer Olstad
- The Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | | | - Hilde Kanli Galtung
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
| | - Tor Paaske Utheim
- The Regenerative Medicine Unit, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, 0372 Oslo, Norway
- Department of Ophthalmology, Oslo University Hospital, 0450 Oslo, Norway
- Department of Ophthalmology, Sørlandet Hospital Arendal, 4838 Arendal, Norway
- Department of Ophthalmology, Vestre Viken Hospital Trust, 3004 Drammen, Norway
- The Norwegian Dry Eye Clinic, 0369 Oslo, Norway
| | - Janicke Liaaen Jensen
- Department of Oral Surgery and Oral Medicine, Faculty of Dentistry, University of Oslo, 0455 Oslo, Norway
| | - Reidun Øvstebø
- The Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
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Abstract
tRNAs are key adaptor molecules that decipher the genetic code during translation of mRNAs in protein synthesis. In contrast to the traditional view of tRNAs as ubiquitously expressed housekeeping molecules, awareness is now growing that tRNA-encoding genes display tissue-specific and cell type-specific patterns of expression, and that tRNA gene expression and function are both dynamically regulated by post-transcriptional RNA modifications. Moreover, dysregulation of tRNAs, mediated by alterations in either their abundance or function, can have deleterious consequences that contribute to several distinct human diseases, including neurological disorders and cancer. Accumulating evidence shows that reprogramming of mRNA translation through altered tRNA activity can drive pathological processes in a codon-dependent manner. This Review considers the emerging evidence in support of the precise control of functional tRNA levels as an important regulatory mechanism that coordinates mRNA translation and protein expression in physiological cell homeostasis, and highlights key examples of human diseases that are linked directly to tRNA dysregulation.
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Affiliation(s)
- Esteban A Orellana
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Elisabeth Siegal
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
- Harvard Initiative for RNA Medicine, Harvard University, Boston, MA, USA.
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Shen X, Dong N, Xu Y, Han L, Yang R, Liao J, Zhang X, Xie T, Wang Y, Chen C, Liu M, Jiang Y, Yu L, Fang Q. Analyzing Corin–BNP–NEP Protein Pathway Revealing Differential Mechanisms in AF-Related Ischemic Stroke and No AF-Related Ischemic Stroke. Front Aging Neurosci 2022; 14:863489. [PMID: 35615592 PMCID: PMC9125077 DOI: 10.3389/fnagi.2022.863489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Background The incidence of atrial fibrillation (AF)-related stroke increases with aging. Natriuretic peptides (NPs) family, including Corin-B type natriuretic peptide (BNP)-neprilysin (NEP) protein levels increased with age and are risk markers of cardiovascular and cerebrovascular diseases, such as AF and cardioembolic stroke. Aging is also linked to epigenetics, specifically DNA methylation. However, only a few studies have investigated the effect of DNA methylation on the NP system. Thus, the present study aimed to investigate whether the Corin-BNP-NEP protein pathway is involved in the pathogenesis of AF-stroke and CpG methylation in the promoter region of the Corin protein gene has an effect on AF-related ischemic stroke. Methods A total of 82 patients hospitalized with acute ischemic strokes were enrolled in this study. The differences in clinical information were compared between the AF-stroke (n = 37) and no AF-stroke groups (n = 45). Plasma-soluble Corin and NEP were detected using an ELISA kit. CpG methylation in the promoter region of the gene was assessed by a next-generation sequencing-based bisulfite sequencing polymerase chain reaction (BSP). Results (1) Patients in AF-stroke were older, had higher initial NIHSS score, 90-day mRs, higher D2-dimer, INR, and APTT, and low TG, TC, and HbA1c (all p < 0.05). (2) Serum levels of Corin and BNP in the AF-stroke group were significantly higher than that in the no AF-stroke group (p < 0.05). No significant difference was detected in the serum levels of NEP between the two groups. (3) The levels of CpG methylation in the promoter region of the Corin protein gene in the AF-stroke group was significantly lower than that in the no AF-stroke group (p < 0.05). The CpG sites with maximal methylation differences between the two groups were CORIN:678, CORIN:682, CORIN:694, and CORIN:700. Conclusion The current findings raise the possibility that the Corin–BNP–NEP protein pathway may be involved in the pathogenesis of AF-related ischemic stroke. Deficient CpG methylation in the promoter region of the Corin protein gene is associated with AF-related ischemic stroke.
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Affiliation(s)
- Xiaozhu Shen
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Geriatrics, Lianyungang Second People’s Hospital, Lianyungang, China
| | - Nan Dong
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Neurology, Suzhou Industrial Park Xinghai Hospital, Suzhou, China
| | - Yiwen Xu
- Department of General Medicine, Lianyungang Hospital, Affiliated to Jiangsu University (Lianyungang Second People’s Hospital), Lianyungang, China
- *Correspondence: Yiwen Xu,
| | - Lin Han
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Rui Yang
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Juan Liao
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xianxian Zhang
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Tao Xie
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yugang Wang
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Chen Chen
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Mengqian Liu
- Department of General Medicine, Lianyungang Hospital, Affiliated to Jiangsu University (Lianyungang Second People’s Hospital), Lianyungang, China
| | - Yi Jiang
- Bengbu Medical College, Bengbu, China
| | - Liqiang Yu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Qi Fang
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Qi Fang,
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Goldkamp AK, Li Y, Rivera RM, Hagen DE. Characterization of tRNA expression profiles in large offspring syndrome. BMC Genomics 2022; 23:273. [PMID: 35392796 PMCID: PMC8988405 DOI: 10.1186/s12864-022-08496-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/23/2022] [Indexed: 11/10/2022] Open
Abstract
Background Assisted Reproductive Technologies (ART) use can increase the risk of congenital overgrowth syndromes, such as large offspring syndrome (LOS) in ruminants. Epigenetic variations are known to influence gene expression and differentially methylated regions (DMRs) were previously determined to be associated with LOS in cattle. We observed DMRs overlapping tRNA clusters which could affect tRNA abundance and be associated with tissue specificity or overgrowth. Variations in tRNA expression have been identified in several disease pathways suggesting an important role in the regulation of biological processes. Understanding the role of tRNA expression in cattle offers an opportunity to reveal mechanisms of regulation at the translational level. We analyzed tRNA expression in the skeletal muscle and liver tissues of day 105 artificial insemination-conceived, ART-conceived with a normal body weight, and ART-conceived bovine fetuses with a body weight above the 97th percentile compared to Control-AI. Results Despite the centrality of tRNAs to translation, in silico predictions have revealed dramatic differences in the number of tRNA genes between humans and cattle (597 vs 1,659). Consistent with reports in human, only a fraction of predicted tRNA genes are expressed. We detected the expression of 474 and 487 bovine tRNA genes in the muscle and liver with the remainder being unexpressed. 193 and 198 unique tRNA sequences were expressed in all treatment groups within muscle and liver respectively. In addition, an average of 193 tRNA sequences were expressed within the same treatment group in different tissues. Some tRNA isodecoders were differentially expressed between treatment groups. In the skeletal muscle and liver, we categorized 11 tRNA isoacceptors with undetected expression as well as an isodecoder that was unexpressed in the liver (SerGGA). Our results identified variation in the proportion of tRNA gene copies expressed between tissues and differences in the highest contributing tRNA anticodon within an amino acid family due to treatment and tissue type. Out of all amino acid families, roughly half of the most highly expressed tRNA isoacceptors correlated to their most frequent codon in the bovine genome. Conclusion Although the number of bovine tRNA genes is nearly triple of that of the tRNA genes in human, there is a shared occurrence of transcriptionally inactive tRNA genes in both species. We detected differential expression of tRNA genes as well as tissue- and treatment- specific tRNA transcripts with unique sequence variations that could modulate translation during protein homeostasis or cellular stress, and give rise to regulatory products targeting genes related to overgrowth in the skeletal muscle and/or tumor development in the liver of LOS individuals. While the absence of certain isodecoders may be relieved by wobble base pairing, missing tRNA species could increase the likelihood of mistranslation or mRNA degradation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08496-7.
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Affiliation(s)
- Anna K Goldkamp
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Yahan Li
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Rocio M Rivera
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Darren E Hagen
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA.
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