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Raitoharju E, Rajić S, Marttila S. Non-coding 886 ( nc886/ vtRNA2-1), the epigenetic odd duck - implications for future studies. Epigenetics 2024; 19:2332819. [PMID: 38525792 DOI: 10.1080/15592294.2024.2332819] [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: 12/08/2023] [Accepted: 03/14/2024] [Indexed: 03/26/2024] Open
Abstract
Non-coding 886 (nc886, vtRNA2-1) is the only human polymorphically imprinted gene, in which the methylation status is not determined by genetics. Existing literature regarding the establishment, stability and consequences of the methylation pattern, as well as the nature and function of the nc886 RNAs transcribed from the locus, are contradictory. For example, the methylation status of the locus has been reported to be stable through life and across somatic tissues, but also susceptible to environmental effects. The nature of the produced nc886 RNA(s) has been redefined multiple times, and in carcinogenesis, these RNAs have been reported to have conflicting roles. In addition, due to the bimodal methylation pattern of the nc886 locus, traditional genome-wide methylation analyses can lead to false-positive results, especially in smaller datasets. Herein, we aim to summarize the existing literature regarding nc886, discuss how the characteristics of nc886 give rise to contradictory results, as well as to reinterpret, reanalyse and, where possible, replicate the results presented in the current literature. We also introduce novel findings on how the distribution of the nc886 methylation pattern is associated with the geographical origins of the population and describe the methylation changes in a large variety of human tumours. Through the example of this one peculiar genetic locus and RNA, we aim to highlight issues in the analysis of DNA methylation and non-coding RNAs in general and offer our suggestions for what should be taken into consideration in future analyses.
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Affiliation(s)
- Emma Raitoharju
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tays Research Services, Wellbeing Services County of Pirkanmaa, Tampere University Hospital, Tampere, Finland
| | - Sonja Rajić
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Saara Marttila
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tays Research Services, Wellbeing Services County of Pirkanmaa, Tampere University Hospital, Tampere, Finland
- Gerontology Research Center, Tampere University, Tampere, Finland
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Taube M, Lisiak N, Totoń E, Rubiś B. Human Vault RNAs: Exploring Their Potential Role in Cellular Metabolism. Int J Mol Sci 2024; 25:4072. [PMID: 38612882 PMCID: PMC11012908 DOI: 10.3390/ijms25074072] [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: 03/07/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
Non-coding RNAs have been described as crucial regulators of gene expression and guards of cellular homeostasis. Some recent papers focused on vault RNAs, one of the classes of non-coding RNA, and their role in cell proliferation, tumorigenesis, apoptosis, cancer response to therapy, and autophagy, which makes them potential therapy targets in oncology. In the human genome, four vault RNA paralogues can be distinguished. They are associated with vault complexes, considered the largest ribonucleoprotein complexes. The protein part of these complexes consists of a major vault protein (MVP) and two minor vault proteins (vPARP and TEP1). The name of the complex, as well as vault RNA, comes from the hollow barrel-shaped structure that resembles a vault. Their sequence and structure are highly evolutionarily conserved and show many similarities in comparison with different species, but vault RNAs have various roles. Vaults were discovered in 1986, and their functions remained unclear for many years. Although not much is known about their contribution to cell metabolism, it has become clear that vault RNAs are involved in various processes and pathways associated with cancer progression and modulating cell functioning in normal and pathological stages. In this review, we discuss known functions of human vault RNAs in the context of cellular metabolism, emphasizing processes related to cancer and cancer therapy efficacy.
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Affiliation(s)
| | | | | | - Błażej Rubiś
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, Rokietnicka 3, 60-806 Poznan, Poland; (M.T.); (N.L.); (E.T.)
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Avila-Bonilla RG, Martínez-Montero JP. Crosstalk between vault RNAs and innate immunity. Mol Biol Rep 2024; 51:387. [PMID: 38443657 PMCID: PMC10914904 DOI: 10.1007/s11033-024-09305-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: 11/15/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024]
Abstract
PURPOSE Vault (vt) RNAs are noncoding (nc) RNAs transcribed by RNA polymerase III (RNA Pol III) with 5'-triphosphate (5'-PPP) termini that play significant roles and are recognized by innate immune sensors, including retinoic acid-inducible protein 1 (RIG-I). In addition, vtRNAs adopt secondary structures that can be targets of interferon-inducible protein kinase R (PKR) and the oligoadenylate synthetase (OAS)/RNase L system, both of which are important for activating antiviral defenses. However, changes in the expression of vtRNAs have been associated with pathological processes that activate proinflammatory pathways, which influence cellular events such as differentiation, aging, autophagy, apoptosis, and drug resistance in cancer cells. RESULTS In this review, we summarized the biology of vtRNAs and focused on their interactions with the innate immune system. These findings provide insights into the diverse roles of vtRNAs and their correlation with various cellular processes to improve our understanding of their biological functions.
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Affiliation(s)
- Rodolfo Gamaliel Avila-Bonilla
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Departamento de Genética y Biología Molecular, Av. IPN 2508, 07360, Mexico City, Mexico.
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Aghajani Mir M. Vault RNAs (vtRNAs): Rediscovered non-coding RNAs with diverse physiological and pathological activities. Genes Dis 2024; 11:772-787. [PMID: 37692527 PMCID: PMC10491885 DOI: 10.1016/j.gendis.2023.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 01/16/2023] [Indexed: 04/05/2023] Open
Abstract
The physicochemical characteristics of RNA admit non-coding RNAs to perform a different range of biological acts through various mechanisms and are involved in regulating a diversity of fundamental processes. Notably, some reports of pathological conditions have proved abnormal expression of many non-coding RNAs guides the ailment. Vault RNAs are a class of non-coding RNAs containing stem regions or loops with well-conserved sequence patterns that play a fundamental role in the function of vault particles through RNA-ligand, RNA-RNA, or RNA-protein interactions. Taken together, vault RNAs have been proposed to be involved in a variety of functions such as cell proliferation, nucleocytoplasmic transport, intracellular detoxification processes, multidrug resistance, apoptosis, and autophagy, and serve as microRNA precursors and signaling pathways. Despite decades of investigations devoted, the biological function of the vault particle or the vault RNAs is not yet completely cleared. In this review, the current scientific assertions of the vital vault RNAs functions were discussed.
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Affiliation(s)
- Mahsa Aghajani Mir
- Deputy of Research and Technology, Health Research Institute, Babol University of Medical Sciences, Babol 47176-4774, Iran
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Mattijssen S, Kerkhofs K, Stephen J, Yang A, Han CG, Tadafumi Y, Iben JR, Mishra S, Sakhawala RM, Ranjan A, Gowda M, Gahl WA, Gu S, Malicdan MC, Maraia RJ. A POLR3B-variant reveals a Pol III transcriptome response dependent on La protein/SSB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.577363. [PMID: 38410490 PMCID: PMC10896340 DOI: 10.1101/2024.02.05.577363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
RNA polymerase III (Pol III, POLR3) synthesizes tRNAs and other small non-coding RNAs. Human POLR3 pathogenic variants cause a range of developmental disorders, recapitulated in part by mouse models, yet some aspects of POLR3 deficiency have not been explored. We characterized a human POLR3B:c.1625A>G;p.(Asn542Ser) disease variant that was found to cause mis-splicing of POLR3B. Genome-edited POLR3B1625A>G HEK293 cells acquired the mis-splicing with decreases in multiple POLR3 subunits and TFIIIB, although display auto-upregulation of the Pol III termination-reinitiation subunit POLR3E. La protein was increased relative to its abundant pre-tRNA ligands which bind via their U(n)U-3'-termini. Assays for cellular transcription revealed greater deficiencies for tRNA genes bearing terminators comprised of 4Ts than of ≥5Ts. La-knockdown decreased Pol III ncRNA expression unlinked to RNA stability. Consistent with these effects, small-RNAseq showed that POLR3B1625A>G and patient fibroblasts express more tRNA fragments (tRFs) derived from pre-tRNA 3'-trailers (tRF-1) than from mature-tRFs, and higher levels of multiple miRNAs, relative to control cells. The data indicate that decreased levels of Pol III transcripts can lead to functional excess of La protein which reshapes small ncRNA profiles revealing new depth in the Pol III system. Finally, patient cell RNA analysis uncovered a strategy for tRF-1/tRF-3 as POLR3-deficiency biomarkers.
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Affiliation(s)
- Sandy Mattijssen
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Kyra Kerkhofs
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Joshi Stephen
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Acong Yang
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, 21702 USA
| | - Chen G. Han
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Yokoyama Tadafumi
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - James R. Iben
- Molecular Genetics Core, NICHD, NIH, Bethesda, MD 20892, USA
| | - Saurabh Mishra
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Rima M. Sakhawala
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Amitabh Ranjan
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Mamatha Gowda
- Department of Obstetrics & Gynaecology, Jawaharlal Institute of Post-Graduate Medical Education and Research, Puducherry, India
| | - William A. Gahl
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- NIH Undiagnosed Diseases Program, NIH, Bethesda, MD 20892, USA
| | - Shuo Gu
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, 21702 USA
| | - May C. Malicdan
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- NIH Undiagnosed Diseases Program, NIH, Bethesda, MD 20892, USA
| | - Richard J. Maraia
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
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Small but Powerful: The Human Vault RNAs as Multifaceted Modulators of Pro-Survival Characteristics and Tumorigenesis. Cancers (Basel) 2022; 14:cancers14112787. [PMID: 35681764 PMCID: PMC9179338 DOI: 10.3390/cancers14112787] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/23/2022] [Accepted: 06/01/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary Small non-protein-coding RNAs have been recognized as valuable regulators of gene expression in all three domains of life. Particularly in multicellular organisms, ncRNAs-mediated gene expression control has evolved as a central principle of cellular homeostasis. Thus, it is not surprising that non-coding RNA misregulation has been linked to various diseases. Here, we review the contributions of the four human vault RNAs to cellular proliferation, apoptosis and cancer biology. Abstract The importance of non-coding RNAs for regulating gene expression has been uncovered in model systems spanning all three domains of life. More recently, their involvement in modulating signal transduction, cell proliferation, tumorigenesis and cancer progression has also made them promising tools and targets for oncotherapy. Recent studies revealed a class of highly conserved small ncRNAs, namely vault RNAs, as regulators of several cellular homeostasis mechanisms. The human genome encodes four vault RNA paralogs that share significant sequence and structural similarities, yet they seem to possess distinct roles in mammalian cells. The alteration of vault RNA expression levels has frequently been observed in cancer tissues, thus hinting at a putative role in orchestrating pro-survival characteristics. Over the last decade, significant advances have been achieved in clarifying the relationship between vault RNA and cellular mechanisms involved in cancer development. It became increasingly clear that vault RNAs are involved in controlling apoptosis, lysosome biogenesis and function, as well as autophagy in several malignant cell lines, most likely by modulating signaling pathways (e.g., the pro-survival MAPK cascade). In this review, we discuss the identified and known functions of the human vault RNAs in the context of cell proliferation, tumorigenesis and chemotherapy resistance.
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Fort RS, Duhagon MA. Pan-cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology. F1000Res 2021; 10:182. [PMID: 34354812 PMCID: PMC8287541 DOI: 10.12688/f1000research.28510.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 12/17/2022] Open
Abstract
Background: The vault RNAs (vtRNAs) are a class of 84-141-nt eukaryotic non-coding RNAs transcribed by RNA polymerase III, associated to the ribonucleoprotein complex known as vault particle. Of the four human vtRNA genes, vtRNA1-1, vtRNA1-2 and vtRNA1-3, clustered at locus 1, are integral components of the vault particle, while vtRNA2-1 is a more divergent homologue located in a second locus. Gene expression studies of vtRNAs in large cohorts have been hindered by their unsuccessful sequencing using conventional transcriptomic approaches. Methods: VtRNA expression in The Cancer Genome Atlas (TCGA) Pan-Cancer cohort was estimated using the genome-wide DNA methylation and chromatin accessibility data (ATAC-seq) of their genes as surrogate variables. The association between vtRNA expression and patient clinical outcome, immune subtypes and transcriptionally co-regulated gene programs was analyzed in the dataset. Results: VtRNAs promoters are enriched in transcription factors related to viral infection. VtRNA2-1 is likely the most independently regulated homologue. VtRNA1-1 has the most accessible chromatin, followed by vtRNA1-2, vtRNA2-1 and vtRNA1-3. VtRNA1-1 and vtRNA1-3 chromatin status does not significantly change in cancer tissues. Meanwhile, vtRNA2-1 and vtRNA1-2 expression is widely deregulated in neoplastic tissues and its alteration is compatible with a broad oncogenic role for vtRNA1-2, and both tumor suppressor and oncogenic functions for vtRNA2-1. Yet, vtRNA1-1, vtRNA1-2 and vtRNA2-1 promoter DNA methylation predicts a shorter patient overall survival cancer-wide. In addition, gene ontology analyses of vtRNAs co-regulated genes identify a chromosome regulatory domain, epithelial differentiation, immune and thyroid cancer gene sets for specific vtRNAs. Furthermore, vtRNA expression patterns are associated with cancer immune subtypes and vtRNA1-2 expression is positively associated with cell proliferation and wound healing. Conclusions: Our study presents the landscape of vtRNA chromatin status cancer-wide, identifying co-regulated gene networks and ontological pathways associated with the different vtRNA genes that may account for their diverse roles in cancer.
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Affiliation(s)
- Rafael Sebastián Fort
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Montevideo, 11400, Uruguay.,Depto. de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Montevideo, 11600, Uruguay
| | - María Ana Duhagon
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Montevideo, 11400, Uruguay.,Depto. de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Montevideo, 11400, Uruguay
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