51
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Kneppers J, Bergman AM, Zwart W. Prostate Cancer Epigenetic Plasticity and Enhancer Heterogeneity: Molecular Causes, Consequences and Clinical Implications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1390:255-275. [DOI: 10.1007/978-3-031-11836-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
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52
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Tan H, Liu T, Zhou T. Exploring the role of eRNA in regulating gene expression. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:2095-2119. [PMID: 35135243 DOI: 10.3934/mbe.2022098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
eRNAs as the products of enhancers can regulate gene expression via various possible ways, but which regulation way is more reasonable is debatable in biology, and in particular, how eRNAs impact gene expression remains unclear. Here we introduce a mechanistic model of gene expression to address these issues. This model considers three possible regulation ways of eRNA: Type-I by which eRNA regulates transcriptional activity by facilitating the formation of enhancer-promoter (E-P) loop, Type-II by which eRNA directly promotes the mRNA production rate, and mixed regulation (i.e., the combination of Type-I and Type-II). We show that with the increase of the E-P loop length, mRNA distribution can transition from unimodality to bimodality or vice versa in all the three regulation cases. However, in contrast to the other two regulations, Type-II regulation can lead to the highest mean mRNA level and the lowest mRNA noise, independent of the E-P loop length. These results would not only reveal the essential mechanism of how eRNA regulates gene expression, but also imply a new mechanism for phenotypic switching, namely the E-P loop can induce phenotypic switching.
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Affiliation(s)
- Heli Tan
- School of Financial Mathematics and Statistics, Guangdong University of Finance, Guangzhou 510521, China
| | - Tuoqi Liu
- School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, China
| | - Tianshou Zhou
- School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, China
- Guangdong Province Key Laboratory of Computational Science, Guangzhou 510275, China
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53
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Panes JD, Wendt A, Ramirez-Molina O, Castro PA, Fuentealba J. Deciphering the role of PGC-1α in neurological disorders: from mitochondrial dysfunction to synaptic failure. Neural Regen Res 2022; 17:237-245. [PMID: 34269182 PMCID: PMC8463972 DOI: 10.4103/1673-5374.317957] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The onset and mechanisms underlying neurodegenerative diseases remain uncertain. The main features of neurodegenerative diseases have been related with cellular and molecular events like neuronal loss, mitochondrial dysfunction and aberrant accumulation of misfolded proteins or peptides in specific areas of the brain. The most prevalent neurodegenerative diseases belonging to age-related pathologies are Alzheimer's disease, Huntington's disease, Parkinson's disease and amyotrophic lateral sclerosis. Interestingly, mitochondrial dysfunction has been observed to occur during the early onset of several neuropathological events associated to neurodegenerative diseases. The master regulator of mitochondrial quality control and energetic metabolism is the transcriptional coactivator peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α). Additionally, it has been observed that PGC-1α appears to be a key factor in maintaining neuronal survival and synaptic transmission. In fact, PGC-1α downregulation in different brain areas (hippocampus, substantia nigra, cortex, striatum and spinal cord) that occurs in function of neurological damage including oxidative stress, neuronal loss, and motor disorders has been seen in several animal and cellular models of neurodegenerative diseases. Current evidence indicates that PGC-1α upregulation may serve as a potent therapeutic approach against development and progression of neuronal damage. Remarkably, increasing evidence shows that PGC-1α deficient mice have neurodegenerative diseases-like features, as well as neurological abnormalities. Finally, we discuss recent studies showing novel specific PGC-1α isoforms in the central nervous system that appear to exert a key role in the age of onset of neurodegenerative diseases and have a neuroprotective function in the central nervous system, thus opening a new molecular strategy for treatment of neurodegenerative diseases. The purpose of this review is to provide an up-to-date overview of the PGC-1α role in the physiopathology of neurodegenerative diseases, as well as establish the importance of PGC-1α function in synaptic transmission and neuronal survival.
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Affiliation(s)
- Jessica D Panes
- Laboratorio de Screening de Compuestos Neuroactivos (LSCN), Departamento de Fisiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Aline Wendt
- Laboratorio de Screening de Compuestos Neuroactivos (LSCN), Departamento de Fisiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Oscar Ramirez-Molina
- Laboratorio de Screening de Compuestos Neuroactivos (LSCN), Departamento de Fisiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Patricio A Castro
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Jorge Fuentealba
- Laboratorio de Screening de Compuestos Neuroactivos (LSCN), Departamento de Fisiología; Centro de Investigaciones Avanzadas en Biomedicina (CIAB-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
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54
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Cayir A. RNA modifications as emerging therapeutic targets. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 13:e1702. [PMID: 34816607 DOI: 10.1002/wrna.1702] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 12/11/2022]
Abstract
The field of epitranscriptome, posttranscriptional modifications to RNAs, is still growing up and has presented substantial evidences for the role of RNA modifications in diseases. In terms of new drug development, RNA modifications have a great promise for therapy. For example, more than 170 type of modifications exist in various types of RNAs. Regulatory genes and their roles in critical biological process have been identified and they are associated with several diseases. Current data, for example, identification of inhibitors targeting RNA modifications regulatory genes, strongly support the idea that RNA modifications have potential as emerging therapeutic targets. Therefore, in this review, RNA modifications and regulatory genes were comprehensively documented in terms of drug development by summarizing the findings from previous studies. It was discussed how RNA modifications or regulatory genes can be targeted by altering molecular mechanisms. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Akin Cayir
- Vocational Health College, Canakkale Onsekiz Mart University, Canakkale, Turkey.,Akershus Universitetssykehus, Medical Department, Lørenskog, Norway
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55
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RNA Modifications and RNA Metabolism in Neurological Disease Pathogenesis. Int J Mol Sci 2021; 22:ijms222111870. [PMID: 34769301 PMCID: PMC8584444 DOI: 10.3390/ijms222111870] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/16/2021] [Accepted: 10/26/2021] [Indexed: 02/06/2023] Open
Abstract
The intrinsic cellular heterogeneity and molecular complexity of the mammalian nervous system relies substantially on the dynamic nature and spatiotemporal patterning of gene expression. These features of gene expression are achieved in part through mechanisms involving various epigenetic processes such as DNA methylation, post-translational histone modifications, and non-coding RNA activity, amongst others. In concert, another regulatory layer by which RNA bases and sugar residues are chemically modified enhances neuronal transcriptome complexity. Similar RNA modifications in other systems collectively constitute the cellular epitranscriptome that integrates and impacts various physiological processes. The epitranscriptome is dynamic and is reshaped constantly to regulate vital processes such as development, differentiation and stress responses. Perturbations of the epitranscriptome can lead to various pathogenic conditions, including cancer, cardiovascular abnormalities and neurological diseases. Recent advances in next-generation sequencing technologies have enabled us to identify and locate modified bases/sugars on different RNA species. These RNA modifications modulate the stability, transport and, most importantly, translation of RNA. In this review, we discuss the formation and functions of some frequently observed RNA modifications—including methylations of adenine and cytosine bases, and isomerization of uridine to pseudouridine—at various layers of RNA metabolism, together with their contributions to abnormal physiological conditions that can lead to various neurodevelopmental and neurological disorders.
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56
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Kumari K, Groza P, Aguilo F. Regulatory roles of RNA modifications in breast cancer. NAR Cancer 2021; 3:zcab036. [PMID: 34541538 PMCID: PMC8445368 DOI: 10.1093/narcan/zcab036] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/07/2021] [Accepted: 08/25/2021] [Indexed: 12/14/2022] Open
Abstract
Collectively referred to as the epitranscriptome, RNA modifications play important roles in gene expression control regulating relevant cellular processes. In the last few decades, growing numbers of RNA modifications have been identified not only in abundant ribosomal (rRNA) and transfer RNA (tRNA) but also in messenger RNA (mRNA). In addition, many writers, erasers and readers that dynamically regulate the chemical marks have also been characterized. Correct deposition of RNA modifications is prerequisite for cellular homeostasis, and its alteration results in aberrant transcriptional programs that dictate human disease, including breast cancer, the most frequent female malignancy, and the leading cause of cancer-related death in women. In this review, we emphasize the major RNA modifications that are present in tRNA, rRNA and mRNA. We have categorized breast cancer-associated chemical marks and summarize their contribution to breast tumorigenesis. In addition, we describe less abundant tRNA modifications with related pathways implicated in breast cancer. Finally, we discuss current limitations and perspectives on epitranscriptomics for use in therapeutic strategies against breast and other cancers.
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Affiliation(s)
- Kanchan Kumari
- Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden
| | - Paula Groza
- Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden
| | - Francesca Aguilo
- Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden
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57
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Zhang Q, Liu F, Chen W, Miao H, Liang H, Liao Z, Zhang Z, Zhang B. The role of RNA m 5C modification in cancer metastasis. Int J Biol Sci 2021; 17:3369-3380. [PMID: 34512153 PMCID: PMC8416729 DOI: 10.7150/ijbs.61439] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 07/19/2021] [Indexed: 12/26/2022] Open
Abstract
Epigenetic modification plays a crucial regulatory role in the biological processes of eukaryotic cells. The recent characterization of DNA and RNA methylation is still ongoing. Tumor metastasis has long been an unconquerable feature in the fight against cancer. As an inevitable component of the epigenetic regulatory network, 5-methylcytosine is associated with multifarious cellular processes and systemic diseases, including cell migration and cancer metastasis. Recently, gratifying progress has been achieved in determining the molecular interactions between m5C writers (DNMTs and NSUNs), demethylases (TETs), readers (YTHDF2, ALYREF and YBX1) and RNAs. However, the underlying mechanism of RNA m5C methylation in cell mobility and metastasis remains unclear. The functions of m5C writers and readers are believed to regulate gene expression at the post-transcription level and are involved in cellular metabolism and movement. In this review, we emphatically summarize the recent updates on m5C components and related regulatory networks. The content will be focused on writers and readers of the RNA m5C modification and potential mechanisms in diseases. We will discuss relevant upstream and downstream interacting molecules and their associations with cell migration and metastasis.
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Affiliation(s)
- Qiaofeng Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.,Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei 430030, China.,Hubei key laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Furong Liu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.,Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei 430030, China.,Hubei key laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Wei Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.,Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei 430030, China.,Hubei key laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Hongrui Miao
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.,Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei 430030, China.,Hubei key laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Huifang Liang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.,Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei 430030, China.,Hubei key laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Zhibin Liao
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.,Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei 430030, China.,Hubei key laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Zhanguo Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.,Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei 430030, China.,Hubei key laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Bixiang Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.,Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei 430030, China.,Hubei key laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
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58
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Pérez-Schindler J, Kohl B, Schneider-Heieck K, Leuchtmann AB, Henríquez-Olguín C, Adak V, Maier G, Delezie J, Sakoparnig T, Vargas-Fernández E, Karrer-Cardel B, Ritz D, Schmidt A, Hondele M, Jensen TE, Hiller S, Handschin C. RNA-bound PGC-1α controls gene expression in liquid-like nuclear condensates. Proc Natl Acad Sci U S A 2021; 118:e2105951118. [PMID: 34465622 PMCID: PMC8433555 DOI: 10.1073/pnas.2105951118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plasticity of cells, tissues, and organs is controlled by the coordinated transcription of biological programs. However, the mechanisms orchestrating such context-specific transcriptional networks mediated by the dynamic interplay of transcription factors and coregulators are poorly understood. The peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) is a prototypical master regulator of adaptive transcription in various cell types. We now uncovered a central function of the C-terminal domain of PGC-1α to bind RNAs and assemble multiprotein complexes including proteins that control gene transcription and RNA processing. These interactions are important for PGC-1α recruitment to chromatin in transcriptionally active liquid-like nuclear condensates. Notably, such a compartmentalization of active transcription mediated by liquid-liquid phase separation was observed in mouse and human skeletal muscle, revealing a mechanism by which PGC-1α regulates complex transcriptional networks. These findings provide a broad conceptual framework for context-dependent transcriptional control of phenotypic adaptations in metabolically active tissues.
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Affiliation(s)
| | - Bastian Kohl
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | | | - Carlos Henríquez-Olguín
- Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Volkan Adak
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | - Julien Delezie
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | | | | | - Danilo Ritz
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | - Maria Hondele
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Thomas E Jensen
- Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, University of Copenhagen, 2100 Copenhagen, Denmark
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59
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Gao Y, Fang J. RNA 5-methylcytosine modification and its emerging role as an epitranscriptomic mark. RNA Biol 2021; 18:117-127. [PMID: 34288807 DOI: 10.1080/15476286.2021.1950993] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
5-methylcytosine (m5C) is identified as an abundant and conserved modification in various RNAs, including tRNAs, mRNAs, rRNAs, and other non-coding RNAs. The application of high-throughput sequencing and mass spectrometry allowed for the detection of m5C at a single-nucleotide resolution and at a global abundance separately; this contributes to a better understanding of m5C modification and its biological functions. m5C modification plays critical roles in diverse aspects of RNA processing, including tRNA stability, rRNA assembly, and mRNA translation. Notably, altered m5C modifications and mutated RNA m5C methyltransferases are associated with diverse pathological processes, such as nervous system disorders and cancers. This review may provide new sights of molecular mechanism and functional importance of m5C modification.
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Affiliation(s)
- Yaqi Gao
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jingyuan Fang
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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60
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Enhancer RNA: biogenesis, function, and regulation. Essays Biochem 2021; 64:883-894. [PMID: 33034351 DOI: 10.1042/ebc20200014] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/02/2020] [Accepted: 09/23/2020] [Indexed: 12/30/2022]
Abstract
Enhancers are noncoding DNA elements that are present upstream or downstream of a gene to control its spatial and temporal expression. Specific histone modifications, such as monomethylation on histone H3 lysine 4 (H3K4me1) and H3K27ac, have been widely used to assign enhancer regions in mammalian genomes. In recent years, emerging evidence suggests that active enhancers are bidirectionally transcribed to produce enhancer RNAs (eRNAs). This finding not only adds a new reliable feature to define enhancers but also raises a fundamental question of how eRNAs function to activate transcription. Although some believe that eRNAs are merely transcriptional byproducts, many studies have demonstrated that eRNAs execute crucial tasks in regulating chromatin conformation and transcription activation. In this review, we summarize the current understanding of eRNAs from their biogenesis, functions, and regulation to their pathological significance. Additionally, we discuss the challenges and possible mechanisms of eRNAs in regulated transcription.
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61
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Abstract
Similar to epigenetic DNA and histone modifications, epitranscriptomic modifications (RNA modifications) have emerged as crucial regulators in temporal and spatial gene expression during eukaryotic development. To date, over 170 diverse types of chemical modifications have been identified upon RNA nucleobases. Some of these post-synthesized modifications can be reversibly installed, removed, and decoded by their specific cellular components and play critical roles in different biological processes. Accordingly, dysregulation of RNA modification effectors is tightly orchestrated with developmental processes. Here, we particularly focus on three well-studied RNA modifications, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), and N1-methyladenosine (m1A), and summarize recent knowledge of underlying mechanisms and critical roles of these RNA modifications in stem cell fate determination, embryonic development, and cancer progression, providing a better understanding of the whole association between epitranscriptomic regulation and mammalian development.
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62
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De Paolis V, Lorefice E, Orecchini E, Carissimi C, Laudadio I, Fulci V. Epitranscriptomics: A New Layer of microRNA Regulation in Cancer. Cancers (Basel) 2021; 13:3372. [PMID: 34282776 PMCID: PMC8268402 DOI: 10.3390/cancers13133372] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/30/2021] [Accepted: 06/30/2021] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs are pervasive regulators of gene expression at the post-transcriptional level in metazoan, playing key roles in several physiological and pathological processes. Accordingly, these small non-coding RNAs are also involved in cancer development and progression. Furthermore, miRNAs represent valuable diagnostic and prognostic biomarkers in malignancies. In the last twenty years, the role of RNA modifications in fine-tuning gene expressions at several levels has been unraveled. All RNA species may undergo post-transcriptional modifications, collectively referred to as epitranscriptomic modifications, which, in many instances, affect RNA molecule properties. miRNAs are not an exception, in this respect, and they have been shown to undergo several post-transcriptional modifications. In this review, we will summarize the recent findings concerning miRNA epitranscriptomic modifications, focusing on their potential role in cancer development and progression.
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Affiliation(s)
| | | | | | - Claudia Carissimi
- Dipartimento di Medicina Molecolare, Sapienza Università di Roma, 00161 Rome, Italy; (V.D.P.); (E.L.); (E.O.); (V.F.)
| | - Ilaria Laudadio
- Dipartimento di Medicina Molecolare, Sapienza Università di Roma, 00161 Rome, Italy; (V.D.P.); (E.L.); (E.O.); (V.F.)
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63
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Wood S, Willbanks A, Cheng JX. The Role of RNA Modifications and RNA-modifying Proteins in Cancer Therapy and Drug Resistance. Curr Cancer Drug Targets 2021; 21:326-352. [PMID: 33504307 DOI: 10.2174/1568009621666210127092828] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022]
Abstract
The advent of new genome-wide sequencing technologies has uncovered abnormal RNA modifications and RNA editing in a variety of human cancers. The discovery of reversible RNA N6-methyladenosine (RNA: m6A) by fat mass and obesity-associated protein (FTO) demethylase has led to exponential publications on the pathophysiological functions of m6A and its corresponding RNA modifying proteins (RMPs) in the past decade. Some excellent reviews have summarized the recent progress in this field. Compared to the extent of research into RNA: m6A and DNA 5-methylcytosine (DNA: m5C), much less is known about other RNA modifications and their associated RMPs, such as the role of RNA: m5C and its RNA cytosine methyltransferases (RCMTs) in cancer therapy and drug resistance. In this review, we will summarize the recent progress surrounding the function, intramolecular distribution and subcellular localization of several major RNA modifications, including 5' cap N7-methylguanosine (m7G) and 2'-O-methylation (Nm), m6A, m5C, A-to-I editing, and the associated RMPs. We will then discuss dysregulation of those RNA modifications and RMPs in cancer and their role in cancer therapy and drug resistance.
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Affiliation(s)
- Shaun Wood
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| | - Amber Willbanks
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| | - Jason X Cheng
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
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64
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Setten RL, Chomchan P, Epps EW, Burnett JC, Rossi JJ. CRED9: A differentially expressed elncRNA regulates expression of transcription factor CEBPA. RNA (NEW YORK, N.Y.) 2021; 27:rna.078752.121. [PMID: 34039742 PMCID: PMC8284328 DOI: 10.1261/rna.078752.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
Enhancer RNAs (eRNA) are non-coding transcripts produced from active enhancers and have potential gene regulatory function. CCAAT enhancer-binding protein alpha (CEBPA) is a transcription factor generally involved in metabolism, cell cycle inhibition, hematopoiesis, adipogenesis, hepatogenesis, and is associated with tumorigenesis. In this study, we demonstrate that an enhancer-associated long non-coding RNA (elncRNA), transcribed from an enhancer located 9kb downstream from the transcriptional start site (TSS) of CEBPA, positively regulates the expression of CEBPA. As a result, we named this elncRNA 'CEBPA regulatory elncRNA downstream 9kb' or 'CRED9'. CRED9 expression level positively correlates with CEBPA mRNA expression across multiple cell lines as detected by RT droplet digital PCR. Knockdown of CRED9 resulted in a reduction of CEBPA mRNA expression in Hep3B cells. Additionally, CRED9 knockdown in Hep3B and HepG2 cells resulted in lower CEBPA protein expression. We also found that knockdown of CRED9 in Hep3B cells caused a 57.8% reduction in H3K27ac levels at the +9kb CEBPA enhancer. H3K27ac has previously been described as a marker of active enhancers. Taken together, the evidence presented here supports a previously proposed model whereby, in some contexts, eRNA transcripts are necessary to amplify and maintain H3K27ac levels at a given enhancer. Ultimately, this study adds to the growing body of evidence that elncRNA transcripts have important roles in enhancer function and gene regulation.
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65
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Adhikary S, Roy S, Chacon J, Gadad SS, Das C. Implications of Enhancer Transcription and eRNAs in Cancer. Cancer Res 2021; 81:4174-4182. [PMID: 34016622 DOI: 10.1158/0008-5472.can-20-4010] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 05/03/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022]
Abstract
Despite extensive progress in developing anticancer therapies, therapy resistance remains a major challenge that promotes disease relapse. The changes that lead to therapy resistance can be intrinsically present or may be initiated during treatment. Genetic and epigenetic heterogeneity in tumors make it more challenging to deal with therapy resistance. Recent advances in genome-wide analyses have revealed that the deregulation of distal gene regulatory elements, such as enhancers, appears in several pathophysiological conditions, including cancer. Beyond the conventional function of enhancers in recruiting transcription factors to gene promoters, enhancer elements are also transcribed into noncoding RNAs known as enhancer RNAs (eRNA). Accumulating evidence suggests that uncontrolled enhancer activity with aberrant eRNA expression promotes oncogenesis. Interestingly, tissue-specific, transcribed eRNAs from active enhancers can serve as potential therapeutic targets or biomarkers in several cancer types. This review provides a comprehensive overview of the mechanisms of enhancer transcription and eRNAs as well as their potential roles in cancer and drug resistance.
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Affiliation(s)
- Santanu Adhikary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.,Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Siddhartha Roy
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Jessica Chacon
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, Texas
| | - Shrikanth S Gadad
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, Texas. .,Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, Texas.,Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, Texas.,Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynaecology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India. .,Homi Bhaba National Institute, Mumbai, Maharashtra, India
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66
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Willbanks A, Wood S, Cheng JX. RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases. Genes (Basel) 2021; 12:genes12050627. [PMID: 33922187 PMCID: PMC8145807 DOI: 10.3390/genes12050627] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 02/08/2023] Open
Abstract
Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcriptional levels in normal cell development and human diseases. This review will provide an overview of recent advances in the emerging field of RNA epigenetics, specifically the role of RNA modifications and RNA modifying proteins in chromatin remodeling, transcription activation and RNA processing, as well as translational implications in human diseases.
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67
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Abstract
Mammals undergo regular cycles of fasting and feeding that engage dynamic transcriptional responses in metabolic tissues. Here we review advances in our understanding of the gene regulatory networks that contribute to hepatic responses to fasting and feeding. The advent of sequencing and -omics techniques have begun to facilitate a holistic understanding of the transcriptional landscape and its plasticity. We highlight transcription factors, their cofactors, and the pathways that they impact. We also discuss physiological factors that impinge on these responses, including circadian rhythms and sex differences. Finally, we review how dietary modifications modulate hepatic gene expression programs.
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Affiliation(s)
- Lara Bideyan
- Department of Pathology and Laboratory Medicine, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Biological Chemistry, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Rohith Nagari
- Department of Pathology and Laboratory Medicine, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Biological Chemistry, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Peter Tontonoz
- Department of Pathology and Laboratory Medicine, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Biological Chemistry, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
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68
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Chen YS, Yang WL, Zhao YL, Yang YG. Dynamic transcriptomic m 5 C and its regulatory role in RNA processing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1639. [PMID: 33438329 DOI: 10.1002/wrna.1639] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 11/30/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022]
Abstract
RNA 5-methylcytosine (m5 C) is a prevalent RNA modification in multiple RNA species, including messenger RNAs (mRNAs), transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), and noncoding RNAs (ncRNAs), and broadly distributed from archaea, prokaryotes to eukaryotes. The multiple detecting techniques of m5 C have been developed, such as m5 C-RIP-seq, miCLIP-seq, AZA-IP-seq, RNA-BisSeq, TAWO-seq, and Nanopore sequencing. These high-throughput techniques, combined with corresponding analysis pipeline, provide a precise m5 C landscape contributing to the deciphering of its biological functions. The m5 C modification is distributed along with mRNA and enriched around 5'UTR and 3'UTR, and conserved in tRNAs and rRNAs. It is dynamically regulated by its related enzymes, including methyltransferases (NSUN, DNMT, and TRDMT family members), demethylases (TET families and ALKBH1), and binding proteins (ALYREF and YBX1). So far, accumulative studies have revealed that m5 C participates in a variety of RNA metabolism, including mRNA export, RNA stability, and translation. Depletion of m5 C modification in the organism could cause dysfunction of mitochondria, drawback of stress response, frustration of gametogenesis and embryogenesis, abnormality of neuro and brain development, and has been implicated in cell migration and tumorigenesis. In this review, we provide a comprehensive summary of dynamic regulatory elements of RNA m5 C, including methyltransferases (writers), demethylases (erasers), and binding proteins (readers). We also summarized the related detecting technologies and biological functions of the RNA 5-methylcytosine, and provided future perspectives in m5 C research. This article is categorized under: RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Yu-Sheng Chen
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center For Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Lan Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center For Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Yong-Liang Zhao
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center For Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yun-Gui Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center For Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
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69
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Zhong D, Chen M, Zhang L, Chen H, Shi D, Liu Q, Li H. Aberrant regulation of RNA methylation during spermatogenesis. Reprod Domest Anim 2020; 56:3-11. [PMID: 33174242 DOI: 10.1111/rda.13856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/05/2020] [Indexed: 12/15/2022]
Abstract
Natural modifications of cellular RNA include various chemical modifications, such as N6-methyladenosine (m6 A), which enable the orderly metabolism and function of RNA structural diversity, thereby affecting gene expression. Spermatogenesis is a complex differentiating developmental process, which includes the proliferation of spermatogonial stem cells, spermatocyte meiosis and sperm maturation. Emerging evidence has shown that RNA methylation can influence RNA splicing, exportation and translation, which are controlled in the male germline in order to ensure coordinated gene expression. In this review, we summarize the typical characteristics of different types of RNA methylation during the process of spermatogenesis. In particular, we emphasize the functions of the RNA methylation effectors during the male germ cell development.
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Affiliation(s)
- Dandan Zhong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Mengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Lei Zhang
- Shanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Hong Chen
- Shanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China.,Shanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
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70
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Wnuk M, Slipek P, Dziedzic M, Lewinska A. The Roles of Host 5-Methylcytosine RNA Methyltransferases during Viral Infections. Int J Mol Sci 2020; 21:E8176. [PMID: 33142933 PMCID: PMC7663479 DOI: 10.3390/ijms21218176] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 12/23/2022] Open
Abstract
Eukaryotic 5-methylcytosine RNA methyltransferases catalyze the transfer of a methyl group to the fifth carbon of a cytosine base in RNA sequences to produce 5-methylcytosine (m5C). m5C RNA methyltransferases play a crucial role in the maintenance of functionality and stability of RNA. Viruses have developed a number of strategies to suppress host innate immunity and ensure efficient transcription and translation for the replication of new virions. One such viral strategy is to use host m5C RNA methyltransferases to modify viral RNA and thus to affect antiviral host responses. Here, we summarize the latest findings concerning the roles of m5C RNA methyltransferases, namely, NOL1/NOP2/SUN domain (NSUN) proteins and DNA methyltransferase 2/tRNA methyltransferase 1 (DNMT2/TRDMT1) during viral infections. Moreover, the use of m5C RNA methyltransferase inhibitors as an antiviral therapy is discussed.
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Affiliation(s)
- Maciej Wnuk
- Department of Biotechnology, Institute of Biology and Biotechnology, University of Rzeszow, 35-310 Rzeszow, Poland; (P.S.); (M.D.)
| | | | | | - Anna Lewinska
- Department of Biotechnology, Institute of Biology and Biotechnology, University of Rzeszow, 35-310 Rzeszow, Poland; (P.S.); (M.D.)
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71
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Noncoding RNAs Set the Stage for RNA Polymerase II Transcription. Trends Genet 2020; 37:279-291. [PMID: 33046273 DOI: 10.1016/j.tig.2020.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/24/2022]
Abstract
Effective synthesis of mammalian messenger (m)RNAs depends on many factors that together direct RNA polymerase II (pol II) through the different stages of the transcription cycle and ensure efficient cotranscriptional processing of mRNAs. In addition to the many proteins involved in transcription initiation, elongation, and termination, several noncoding (nc)RNAs also function as global transcriptional regulators. Understanding the mode of action of these non-protein regulators has been an intense area of research in recent years. Here, we describe how these ncRNAs influence key regulatory steps of the transcription process, to affect large numbers of genes. Through direct association with pol II or by modulating the activity of transcription or RNA processing factors, these regulatory RNAs perform critical roles in gene expression.
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72
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Transcriptome-wide analysis of PGC-1α-binding RNAs identifies genes linked to glucagon metabolic action. Proc Natl Acad Sci U S A 2020; 117:22204-22213. [PMID: 32848060 DOI: 10.1073/pnas.2000643117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) is a transcriptional coactivator that controls expression of metabolic/energetic genes, programming cellular responses to nutrient and environmental adaptations such as fasting, cold, or exercise. Unlike other coactivators, PGC-1α contains protein domains involved in RNA regulation such as serine/arginine (SR) and RNA recognition motifs (RRMs). However, the RNA targets of PGC-1α and how they pertain to metabolism are unknown. To address this, we performed enhanced ultraviolet (UV) cross-linking and immunoprecipitation followed by sequencing (eCLIP-seq) in primary hepatocytes induced with glucagon. A large fraction of RNAs bound to PGC-1α were intronic sequences of genes involved in transcriptional, signaling, or metabolic function linked to glucagon and fasting responses, but were not the canonical direct transcriptional PGC-1α targets such as OXPHOS or gluconeogenic genes. Among the top-scoring RNA sequences bound to PGC-1α were Foxo1, Camk1δ, Per1, Klf15, Pln4, Cluh, Trpc5, Gfra1, and Slc25a25 PGC-1α depletion decreased a fraction of these glucagon-induced messenger RNA (mRNA) transcript levels. Importantly, knockdown of several of these genes affected glucagon-dependent glucose production, a PGC-1α-regulated metabolic pathway. These studies show that PGC-1α binds to intronic RNA sequences, some of them controlling transcript levels associated with glucagon action.
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73
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Enhancer RNAs are an important regulatory layer of the epigenome. Nat Struct Mol Biol 2020; 27:521-528. [PMID: 32514177 DOI: 10.1038/s41594-020-0446-0] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 05/07/2020] [Indexed: 12/20/2022]
Abstract
Noncoding RNAs (ncRNAs) direct a remarkable number of diverse functions in development and disease through their regulation of transcription, RNA processing and translation. Leading the charge in the RNA revolution is a class of ncRNAs that are synthesized at active enhancers, called enhancer RNAs (eRNAs). Here, we review recent insights into the biogenesis of eRNAs and the mechanisms underlying their multifaceted functions and consider how these findings could inform future investigations into enhancer transcription and eRNA function.
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74
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Schumann U, Zhang HN, Sibbritt T, Pan A, Horvath A, Gross S, Clark SJ, Yang L, Preiss T. Multiple links between 5-methylcytosine content of mRNA and translation. BMC Biol 2020; 18:40. [PMID: 32293435 PMCID: PMC7158060 DOI: 10.1186/s12915-020-00769-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/11/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND 5-Methylcytosine (m5C) is a prevalent base modification in tRNA and rRNA but it also occurs more broadly in the transcriptome, including in mRNA, where it serves incompletely understood molecular functions. In pursuit of potential links of m5C with mRNA translation, we performed polysome profiling of human HeLa cell lysates and subjected RNA from resultant fractions to efficient bisulfite conversion followed by RNA sequencing (bsRNA-seq). Bioinformatic filters for rigorous site calling were devised to reduce technical noise. RESULTS We obtained ~ 1000 candidate m5C sites in the wider transcriptome, most of which were found in mRNA. Multiple novel sites were validated by amplicon-specific bsRNA-seq in independent samples of either human HeLa, LNCaP and PrEC cells. Furthermore, RNAi-mediated depletion of either the NSUN2 or TRDMT1 m5C:RNA methyltransferases showed a clear dependence on NSUN2 for the majority of tested sites in both mRNAs and noncoding RNAs. Candidate m5C sites in mRNAs are enriched in 5'UTRs and near start codons and are embedded in a local context reminiscent of the NSUN2-dependent m5C sites found in the variable loop of tRNA. Analysing mRNA sites across the polysome profile revealed that modification levels, at bulk and for many individual sites, were inversely correlated with ribosome association. CONCLUSIONS Our findings emphasise the major role of NSUN2 in placing the m5C mark transcriptome-wide. We further present evidence that substantiates a functional interdependence of cytosine methylation level with mRNA translation. Additionally, we identify several compelling candidate sites for future mechanistic analysis.
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Affiliation(s)
- Ulrike Schumann
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, 2601, Australian Captial Territory, Australia
| | - He-Na Zhang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Tennille Sibbritt
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, 2601, Australian Captial Territory, Australia
| | - Anyu Pan
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, 2601, Australian Captial Territory, Australia
| | - Attila Horvath
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, 2601, Australian Captial Territory, Australia
| | - Simon Gross
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, 2601, Australian Captial Territory, Australia
| | - Susan J Clark
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, New South Wales, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, 2010, Australia
| | - Li Yang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, 2601, Australian Captial Territory, Australia.
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, 2010, Australia.
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75
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Rambout X, Cho H, Maquat LE. Transcriptional Coactivator PGC-1α Binding to Newly Synthesized RNA via CBP80: A Nexus for Co- and Posttranscriptional Gene Regulation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:47-54. [PMID: 32295928 DOI: 10.1101/sqb.2019.84.040212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Mammalian cells have many quality-control mechanisms that regulate protein-coding gene expression to ensure proper transcript synthesis, processing, and translation. Should a step in transcript metabolism fail to fulfill requisite spatial, temporal, or structural criteria, including the proper acquisition of RNA-binding proteins, then that step will halt, fail to proceed to the next step, and ultimately result in transcript degradation. Quality-control mechanisms constitute a continuum of processes that initiate in the nucleus and extend to the cytoplasm. Here, we present published and unpublished data for protein-coding genes whose expression is activated by the transcriptional coactivator PGC-1α. We show that PGC-1α movement from chromatin, to which it is recruited by DNA-binding proteins, to CBP80 at the 5' cap of nascent transcripts begins a series of co- and posttranscriptional quality- and quantity-control steps that, in total, ensure proper gene expression.
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Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Hana Cho
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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76
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Yang T, Low JJA, Woon ECY. A general strategy exploiting m5C duplex-remodelling effect for selective detection of RNA and DNA m5C methyltransferase activity in cells. Nucleic Acids Res 2020; 48:e5. [PMID: 31691820 PMCID: PMC7145549 DOI: 10.1093/nar/gkz1047] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 10/07/2019] [Accepted: 10/30/2019] [Indexed: 01/25/2023] Open
Abstract
RNA:5-methylcytosine (m5C) methyltransferases are currently the focus of intense research following a series of high-profile reports documenting their physiological links to several diseases. However, no methods exist which permit the specific analysis of RNA:m5C methyltransferases in cells. Herein, we described how a combination of biophysical studies led us to identify distinct duplex-remodelling effects of m5C on RNA and DNA duplexes. Specifically, m5C induces a C3′-endo to C2′-endo sugar-pucker switch in CpG RNA duplex but triggers a B-to-Z transformation in CpG DNA duplex. Inspired by these different ‘structural signatures’, we developed a m5C-sensitive probe which fluoresces spontaneously in response to m5C-induced sugar-pucker switch, hence useful for sensing RNA:m5C methyltransferase activity. Through the use of this probe, we achieved real-time imaging and flow cytometry analysis of NOP2/Sun RNA methyltransferase 2 (NSUN2) activity in HeLa cells. We further applied the probe to the cell-based screening of NSUN2 inhibitors. The developed strategy could also be adapted for the detection of DNA:m5C methyltransferases. This was demonstrated by the development of DNA m5C-probe which permits the screening of DNA methyltransferase 3A inhibitors. To our knowledge, this study represents not only the first examples of m5C-responsive probes, but also a new strategy for discriminating RNA and DNA m5C methyltransferase activity in cells.
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Affiliation(s)
- Tianming Yang
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, 117543 Singapore
| | - Joanne J A Low
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, 117543 Singapore
| | - Esther C Y Woon
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, 117543 Singapore
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77
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Mahesh A, Khan MIK, Govindaraju G, Verma M, Awasthi S, Chavali PL, Chavali S, Rajavelu A, Dhayalan A. SET7/9 interacts and methylates the ribosomal protein, eL42 and regulates protein synthesis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118611. [DOI: 10.1016/j.bbamcr.2019.118611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/21/2019] [Accepted: 11/13/2019] [Indexed: 12/14/2022]
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78
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Lee JH, Xiong F, Li W. Enhancer RNAs in cancer: regulation, mechanisms and therapeutic potential. RNA Biol 2020; 17:1550-1559. [PMID: 31916476 DOI: 10.1080/15476286.2020.1712895] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Enhancers are distal genomic elements critical for gene regulation and cell identify control during development and diseases. Many human cancers were found to associate with enhancer malfunction, due to genetic and epigenetic alterations, which in some cases directly drive tumour growth. Conventionally, enhancers are known to provide DNA binding motifs to recruit transcription factors (TFs) and to control target genes. However, recent progress found that most, if not all, active enhancers pervasively transcribe noncoding RNAs that are referred to as enhancer RNAs (eRNAs). Increasing evidence points to functional roles of at least a subset of eRNAs in gene regulation in both normal and cancer cells, adding new insights into the action mechanisms of enhancers. eRNA expression was observed to be widespread but also specific to tumour types and individual patients, serving as opportunities to exploit them as potential diagnosis markers or therapeutic targets. In this review, we discuss the brief history of eRNA research, their functional mechanisms and importance in cancer gene regulation, as well as their therapeutic and diagnostic values in cancer. We propose that further studies of eRNAs in cancer will offer a promising 'eRNA targeted therapy' for human cancer intervention.
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Affiliation(s)
- Joo-Hyung Lee
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center , Houston, TX, USA
| | - Feng Xiong
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center , Houston, TX, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center , Houston, TX, USA.,Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth , Houston, TX, USA
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79
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Manning M, Jiang Y, Wang R, Liu L, Rode S, Bonahoom M, Kim S, Yang ZQ. Pan-cancer analysis of RNA methyltransferases identifies FTSJ3 as a potential regulator of breast cancer progression. RNA Biol 2020; 17:474-486. [PMID: 31957540 PMCID: PMC7237164 DOI: 10.1080/15476286.2019.1708549] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
RNA methylation, catalysed by a set of RNA methyltransferases (RNMTs), modulates RNA structures, properties, and biological functions. RNMTs are increasingly documented to be dysregulated in various human diseases, particularly developmental disorders and cancer. However, the genomic and transcriptomic alterations of RNMTs, as well as their functional roles in human cancer, are limited. In this study, we utilized an unbiased approach to examine copy number alterations and mutation rates of 58 RNMTs in more than 10,000 clinical samples across 32 human cancer types. We also investigated these alterations and RNMT expression level as they related to clinical features such as tumour subtype, grade, and survival in a large cohort of tumour samples, focusing on breast cancer. Loss-of-function analysis was performed to examine RNMT candidates with important roles in growth and viability of breast cancer cells. We identified a subset of RNMTs, notably TRMT12, NSUN2, TARBP1, and FTSJ3, that were amplified or mutated in a subset of human cancers. Several RNMTs were significantly associated with breast cancer aggressiveness and poor prognosis. Loss-of-function analysis indicated FTSJ3, a 2'-O-Me methyltransferase, as a candidate RNMT with functional roles in promoting cancer growth and survival. A subset of RNMTs, like FTSJ3, represents promising novel targets for anticancer drug discovery. Our findings provide a framework for further study of the functional consequences of RNMT alterations in human cancer and for developing therapies that target cancer-promoting RNMTs in the future.
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Affiliation(s)
- Morenci Manning
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Yuanyuan Jiang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Rui Wang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Diagnostics of Chinese Medicine, Hebei University of Chinese Medicine, Hebei, China
| | - Lanxin Liu
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Shomita Rode
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Madison Bonahoom
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Seongho Kim
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI, USA
| | - Zeng-Quan Yang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI, USA
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80
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Arnold PR, Wells AD, Li XC. Diversity and Emerging Roles of Enhancer RNA in Regulation of Gene Expression and Cell Fate. Front Cell Dev Biol 2020; 7:377. [PMID: 31993419 PMCID: PMC6971116 DOI: 10.3389/fcell.2019.00377] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/17/2019] [Indexed: 12/27/2022] Open
Abstract
Enhancers are cis-regulatory elements in the genome that cooperate with promoters to control target gene transcription. Unlike promoters, enhancers are not necessarily adjacent to target genes and can exert their functions regardless of enhancer orientations, positions and spatial segregations from target genes. Thus, for a long time, the question as to how enhancers act in a temporal and spatial manner attracted considerable attention. The recent discovery that enhancers are also abundantly transcribed raises interesting questions about the exact roles of enhancer RNA (eRNA) in gene regulation. In this review, we highlight the process of enhancer transcription and the diverse features of eRNA. We review eRNA functions, which include enhancer-promoter looping, chromatin modifying, and transcription regulating. As eRNA are transcribed from active enhancers, they exhibit tissue and lineage specificity, and serve as markers of cell state and function. Finally, we discuss the unique relationship between eRNA and super enhancers in phase separation wherein eRNA may contribute significantly to cell fate decisions.
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Affiliation(s)
- Preston R Arnold
- Texas A&M Health Science Center, College of Medicine, Bryan, TX, United States.,Immunobiology and Transplant Sciences, Department of Surgery, Houston Methodist Hospital, Houston, TX, United States
| | - Andrew D Wells
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Xian C Li
- Immunobiology and Transplant Sciences, Department of Surgery, Houston Methodist Hospital, Houston, TX, United States
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81
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van der Kwast RV, Quax PH, Nossent AY. An Emerging Role for isomiRs and the microRNA Epitranscriptome in Neovascularization. Cells 2019; 9:cells9010061. [PMID: 31881725 PMCID: PMC7017316 DOI: 10.3390/cells9010061] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 02/06/2023] Open
Abstract
Therapeutic neovascularization can facilitate blood flow recovery in patients with ischemic cardiovascular disease, the leading cause of death worldwide. Neovascularization encompasses both angiogenesis, the sprouting of new capillaries from existing vessels, and arteriogenesis, the maturation of preexisting collateral arterioles into fully functional arteries. Both angiogenesis and arteriogenesis are highly multifactorial processes that require a multifactorial regulator to be stimulated simultaneously. MicroRNAs can regulate both angiogenesis and arteriogenesis due to their ability to modulate expression of many genes simultaneously. Recent studies have revealed that many microRNAs have variants with altered terminal sequences, known as isomiRs. Additionally, endogenous microRNAs have been identified that carry biochemically modified nucleotides, revealing a dynamic microRNA epitranscriptome. Both types of microRNA alterations were shown to be dynamically regulated in response to ischemia and are able to influence neovascularization by affecting the microRNA’s biogenesis, or even its silencing activity. Therefore, these novel regulatory layers influence microRNA functioning and could provide new opportunities to stimulate neovascularization. In this review we will highlight the formation and function of isomiRs and various forms of microRNA modifications, and discuss recent findings that demonstrate that both isomiRs and microRNA modifications directly affect neovascularization and vascular remodeling.
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Affiliation(s)
- Reginald V.C.T. van der Kwast
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Paul H.A. Quax
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - A. Yaël Nossent
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Department of Laboratory Medicine and Department of Internal Medicine II, Medical University of Vienna, 1090 Vienna, Austria
- Correspondence:
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82
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Kuznetsova SA, Petrukov KS, Pletnev FI, Sergiev PV, Dontsova OA. RNA (C5-cytosine) Methyltransferases. BIOCHEMISTRY (MOSCOW) 2019; 84:851-869. [PMID: 31522668 DOI: 10.1134/s0006297919080029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The review summarizes the data on pro- and eukaryotic RNA (C5-cytosine) methyltransferases. The structure, intracellular location, RNA targets, and catalytic mechanisms of these enzymes, as well as the functional role of methylated cytosine residues in RNA are presented. The functions of RNA (C5-cytosine) methyltransferases unassociated with their methylation activity are discussed. Special attention is given to the similarities and differences in the structures and mechanisms of action of RNA and DNA methyltransferases. The data on the association of mutations in the RNA (C5-cytosine) methyltransferases genes and human diseases are presented.
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Affiliation(s)
- S A Kuznetsova
- Lomonosov Moscow State University, Institute of Functional Genomics, Moscow, 119234, Russia.
| | - K S Petrukov
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia
| | - F I Pletnev
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, 121205, Moscow Region, Russia.,Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - P V Sergiev
- Lomonosov Moscow State University, Institute of Functional Genomics, Moscow, 119234, Russia.,Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, 121205, Moscow Region, Russia.,Petrov National Medical Research Center of Oncology, St. Petersburg, 197758, Russia
| | - O A Dontsova
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, 121205, Moscow Region, Russia.,Institute of Bioorganic Chemistry, Moscow, 117997, Russia
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83
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Saha S, Murmu KC, Biswas M, Chakraborty S, Basu J, Madhulika S, Kolapalli SP, Chauhan S, Sengupta A, Prasad P. Transcriptomic Analysis Identifies RNA Binding Proteins as Putative Regulators of Myelopoiesis and Leukemia. Front Oncol 2019; 9:692. [PMID: 31448224 PMCID: PMC6691814 DOI: 10.3389/fonc.2019.00692] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/12/2019] [Indexed: 12/26/2022] Open
Abstract
Acute myeloid leukemia (AML) is a common and aggressive hematological malignancy. Acquisition of heterogeneous genetic aberrations and epigenetic dysregulation lead to the transformation of hematopoietic stem cells (HSC) into leukemic stem cells (LSC), which subsequently gives rise to immature blast cells and a leukemic phenotype. LSCs are responsible for disease relapse as current chemotherapeutic regimens are not able to completely eradicate these cellular sub-populations. Therefore, it is critical to improve upon the existing knowledge of LSC specific markers, which would allow for specific targeting of these cells more effectively allowing for their sustained eradication from the cellular milieu. Although significant milestones in decoding the aberrant transcriptional network of various cancers, including leukemia, have been achieved, studies on the involvement of post-transcriptional gene regulation (PTGR) in disease progression are beginning to unfold. RNA binding proteins (RBPs) are key players in mediating PTGR and they regulate the intracellular fate of individual transcripts, from their biogenesis to RNA metabolism, via interactions with RNA binding domains (RBDs). In this study, we have used an integrative approach to systematically profile RBP expression and identify key regulatory RBPs involved in normal myeloid development and AML. We have analyzed RNA-seq datasets (GSE74246) of HSCs, common myeloid progenitors (CMPs), granulocyte-macrophage progenitors (GMPs), monocytes, LSCs, and blasts. We observed that normal and leukemic cells can be distinguished on the basis of RBP expression, which is indicative of their ability to define cellular identity, similar to transcription factors. We identified that distinctly co-expressing modules of RBPs and their subclasses were enriched in hematopoietic stem/progenitor (HSPCs) and differentiated monocytes. We detected expression of DZIP3, an E3 ubiquitin ligase, in HSPCs, knockdown of which promotes monocytic differentiation in cell line model. We identified co-expression modules of RBP genes in LSCs and among these, distinct modules of RBP genes with high and low expression. The expression of several AML-specific RBPs were also validated by quantitative polymerase chain reaction. Network analysis identified densely connected hubs of ribosomal RBP genes (rRBPs) with low expression in LSCs, suggesting the dependency of LSCs on altered ribosome dynamics. In conclusion, our systematic analysis elucidates the RBP transcriptomic landscape in normal and malignant myelopoiesis, and highlights the functional consequences that may result from perturbation of RBP gene expression in these cellular landscapes.
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Affiliation(s)
- Subha Saha
- Epigenetic and Chromatin Biology Unit, Institute of Life Sciences, Bhubaneswar, India
| | - Krushna Chandra Murmu
- Epigenetic and Chromatin Biology Unit, Institute of Life Sciences, Bhubaneswar, India
| | - Mayukh Biswas
- Translational Research Unit of Excellence (TRUE), Stem Cell and Leukemia Laboratory, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, India
| | - Sohini Chakraborty
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| | - Jhinuk Basu
- Epigenetic and Chromatin Biology Unit, Institute of Life Sciences, Bhubaneswar, India
| | - Swati Madhulika
- Epigenetic and Chromatin Biology Unit, Institute of Life Sciences, Bhubaneswar, India
| | | | - Santosh Chauhan
- Cell Biology and Infectious Disease Unit, Institute of Life Sciences, Bhubaneswar, India
| | - Amitava Sengupta
- Translational Research Unit of Excellence (TRUE), Stem Cell and Leukemia Laboratory, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, India
| | - Punit Prasad
- Epigenetic and Chromatin Biology Unit, Institute of Life Sciences, Bhubaneswar, India
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84
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K N H, Okabe J, Mathiyalagan P, Khan AW, Jadaan SA, Sarila G, Ziemann M, Khurana I, Maxwell SS, Du XJ, El-Osta A. Sex-Based Mhrt Methylation Chromatinizes MeCP2 in the Heart. iScience 2019; 17:288-301. [PMID: 31323475 PMCID: PMC6639684 DOI: 10.1016/j.isci.2019.06.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/13/2019] [Accepted: 06/20/2019] [Indexed: 01/15/2023] Open
Abstract
In the heart, primary microRNA-208b (pri-miR-208b) and Myheart (Mhrt) are long non-coding RNAs (lncRNAs) encoded by the cardiac myosin heavy chain genes. Although preclinical studies have shown that lncRNAs regulate gene expression and are protective for pathological hypertrophy, the mechanism underlying sex-based differences remains poorly understood. In this study, we examined DNA- and RNA-methylation-dependent regulation of pri-miR-208b and Mhrt. Expression of pri-miR-208b is elevated in the left ventricle of the female heart. Despite indistinguishable DNA methylation between sexes, the interaction of MeCP2 on chromatin is subject to RNase digestion, highlighting that affinity of the methyl-CG reader is broader than previously thought. A specialized procedure to isolate RNA from soluble cardiac chromatin emphasizes sex-based affinity of an MeCP2 co-repressor complex with Rest and Hdac2. Sex-specific Mhrt methylation chromatinizes MeCP2 at the pri-miR-208b promoter and extends the functional relevance of default transcriptional suppression in the heart. Mechanisms underlying sex-based gene expression are poorly understood Expression of primary miR-208b is independent of DNA methylation in the heart Sex-specific methylation of the long non-coding RNA Mhrt distinguishes MeCP2 Procedures assessing soluble chromatin emphasize RNA-dependent affinities
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Affiliation(s)
- Harikrishnan K N
- Epigenetics in Human Health and Disease, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC 3004, Australia; Baker Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, VIC 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jun Okabe
- Epigenetics in Human Health and Disease, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC 3004, Australia; Baker Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, VIC 3004, Australia
| | - Prabhu Mathiyalagan
- Baker Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, VIC 3004, Australia
| | - Abdul Waheed Khan
- Epigenetics in Human Health and Disease, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC 3004, Australia; Baker Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, VIC 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Sameer A Jadaan
- Epigenetics in Human Health and Disease, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC 3004, Australia; Baker Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, VIC 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Gulcan Sarila
- Epigenetics in Human Health and Disease, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC 3004, Australia; Baker Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, VIC 3004, Australia
| | - Mark Ziemann
- Epigenetics in Human Health and Disease, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC 3004, Australia; Baker Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, VIC 3004, Australia
| | - Ishant Khurana
- Epigenetics in Human Health and Disease, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC 3004, Australia; Baker Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, VIC 3004, Australia
| | - Scott S Maxwell
- Epigenetics in Human Health and Disease, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC 3004, Australia; Baker Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, VIC 3004, Australia
| | - Xiao-Jun Du
- Baker Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, VIC 3004, Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC 3004, Australia; Baker Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, VIC 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, 3/F Lui Che Woo Clinical Sciences Building, 30-32 Ngan Shing Street, Sha Tin, Hong Kong SAR; University College Copenhagen, Faculty of Health, Department of Technology, Biomedical Laboratory Science, Copenhagen, Denmark.
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85
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de Lara JCF, Arzate-Mejía RG, Recillas-Targa F. Enhancer RNAs: Insights Into Their Biological Role. Epigenet Insights 2019; 12:2516865719846093. [PMID: 31106290 PMCID: PMC6505235 DOI: 10.1177/2516865719846093] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 12/15/2022] Open
Abstract
Enhancers play a central role in the transcriptional regulation of metazoans. Almost a decade ago, the discovery of their pervasive transcription into noncoding RNAs, termed enhancer RNAs (eRNAs), opened a whole new field of study. The presence of eRNAs correlates with enhancer activity; however, whether they act as functional molecules remains controversial. Here we review direct experimental evidence supporting a functional role of eRNAs in transcription and provide a general pipeline that could help in the design of experimental approaches to investigate the function of eRNAs. We propose that induction of transcriptional activity at enhancers promotes an increase in its activity by an RNA-mediated titration of regulatory proteins that can impact different processes like chromatin accessibility or chromatin looping. In a few cases, transcripts originating from enhancers have acquired specific molecular functions to regulate gene expression. We speculate that these transcripts are either nonannotated long noncoding RNAs (lncRNAs) or are evolving toward functional lncRNAs. Further work will be needed to comprehend better the biological activity of these transcripts.
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Affiliation(s)
- Josué Cortés-Fernández de Lara
- Departamento de Genética Molecular, Instituto de
Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México,
México
| | - Rodrigo G Arzate-Mejía
- Departamento de Genética Molecular, Instituto de
Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México,
México
| | - Félix Recillas-Targa
- Departamento de Genética Molecular, Instituto de
Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México,
México
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86
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Di Serio F, Torchetti EM, Daròs JA, Navarro B. Reassessment of Viroid RNA Cytosine Methylation Status at the Single Nucleotide Level. Viruses 2019; 11:E357. [PMID: 31003406 PMCID: PMC6521008 DOI: 10.3390/v11040357] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 11/17/2022] Open
Abstract
Composed of a few hundreds of nucleotides, viroids are infectious, circular, non-protein coding RNAs able to usurp plant cellular enzymes and molecular machineries to replicate and move in their hosts. Several secondary and tertiary RNA structural motifs have been implicated in the viroid infectious cycle, but whether modified nucleotides, such as 5C-methylcytosine (m5C), also play a role has not been deeply investigated so far. Here, the possible existence of m5C in both RNA polarity strands of potato spindle tuber viroid and avocado sunblotch viroid -which are representative members of the nucleus- and chloroplast-replicating viroids, respectively- has been assessed at single nucleotide level. We show that a standard bisulfite protocol efficiently used for identifying m5C in cellular RNAs may generate false positive results in the case of the highly structured viroid RNAs. Applying a bisulfite conversion protocol specifically adapted to RNAs with high secondary structure, no m5C was identified in both polarity strands of both viroids, indicating that this specific nucleotide modification does not likely play a role in viroid biology.
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Affiliation(s)
- Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante (CNR), 70126 Bari, Italy.
| | | | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València), 46022 Valencia, Spain.
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante (CNR), 70126 Bari, Italy.
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87
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Luo X, Liao C, Quan J, Cheng C, Zhao X, Bode AM, Cao Y. Posttranslational regulation of PGC-1α and its implication in cancer metabolism. Int J Cancer 2019; 145:1475-1483. [PMID: 30848477 PMCID: PMC6767394 DOI: 10.1002/ijc.32253] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 02/01/2019] [Accepted: 03/04/2019] [Indexed: 12/17/2022]
Abstract
Deregulation of cellular metabolism is well established in cancer. The mitochondria are dynamic organelles and act as the center stage for energy metabolism. Central to mitochondrial regulatory network is peroxisome proliferator-activated receptor γ coactivator 1a (PGC-1α), which serves as a master regulator of mitochondrial proliferation and metabolism. The activity and stability of PGC-1α are subject to dynamic and versatile posttranslational modifications including phosphorylation, ubiquitination, methylation and acetylation in response to metabolic stress and other environmental signals. In this review, we describe the structure of PGC-1α. Then, we discuss recent advances in the posttranslational regulatory machinery of PGC-1α, which affects its transcriptional activity, stability and organelle localization. Furthermore, we address the important roles of PGC-1α in tumorigenesis and malignancy. Finally, we also mention the clinical therapeutic potentials of PGC-1α modulators. A better understanding of the elegant function of PGC-1α in cancer progression could provide novel insights into therapeutic interventions through the targeting of PGC-1α signaling.
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Affiliation(s)
- Xiangjian Luo
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410078, China.,Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, Hunan 410078, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, Hunan 410078, China.,Molecular Imaging Research Center of Central South University, Changsha, Hunan 410078, China
| | - Chaoliang Liao
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410078, China.,Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, Hunan 410078, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, Hunan 410078, China
| | - Jing Quan
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410078, China.,Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, Hunan 410078, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, Hunan 410078, China
| | - Can Cheng
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410078, China.,Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, Hunan 410078, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, Hunan 410078, China
| | - Xu Zhao
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410078, China.,Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, Hunan 410078, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, Hunan 410078, China
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Ya Cao
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410078, China.,Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, Hunan 410078, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, Hunan 410078, China.,Molecular Imaging Research Center of Central South University, Changsha, Hunan 410078, China
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88
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Sulaiman SA, Muhsin NIA, Jamal R. Regulatory Non-coding RNAs Network in Non-alcoholic Fatty Liver Disease. Front Physiol 2019; 10:279. [PMID: 30941061 PMCID: PMC6433939 DOI: 10.3389/fphys.2019.00279] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/04/2019] [Indexed: 12/12/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) spectrum comprises simple steatosis and non-alcoholic steatohepatitis (NASH) that can lead to fibrosis and cirrhosis. The patients usually have no history of excessive alcohol consumption and other etiologies that can cause fatty liver. Understanding of the pathophysiology of NAFLD has revealed that non-coding RNAs (ncRNAs) play significant roles in modulating the disease susceptibility, pathogenesis and progression. Currently, the ncRNAs are grouped according to their sizes and their regulatory or housekeeping functions. Each of these ncRNAs has a wide range of involvement in the regulation of the genes and biological pathways. Here, we briefly review the current literature the regulatory ncRNAs in NAFLD pathogenesis and progression, mainly the microRNAs, long non-coding RNAs and circular RNAs. We also discuss the co-regulatory functions and interactions between these ncRNAs in modulating the disease pathogenesis. Elucidation of ncRNAs in NAFLD may facilitate the identification of early diagnostic biomarkers and development of therapeutic strategies for NAFLD.
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Affiliation(s)
- Siti Aishah Sulaiman
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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89
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de Crécy-Lagard V, Boccaletto P, Mangleburg CG, Sharma P, Lowe TM, Leidel SA, Bujnicki JM. Matching tRNA modifications in humans to their known and predicted enzymes. Nucleic Acids Res 2019; 47:2143-2159. [PMID: 30698754 PMCID: PMC6412123 DOI: 10.1093/nar/gkz011] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/28/2018] [Accepted: 01/10/2019] [Indexed: 12/25/2022] Open
Abstract
tRNA are post-transcriptionally modified by chemical modifications that affect all aspects of tRNA biology. An increasing number of mutations underlying human genetic diseases map to genes encoding for tRNA modification enzymes. However, our knowledge on human tRNA-modification genes remains fragmentary and the most comprehensive RNA modification database currently contains information on approximately 20% of human cytosolic tRNAs, primarily based on biochemical studies. Recent high-throughput methods such as DM-tRNA-seq now allow annotation of a majority of tRNAs for six specific base modifications. Furthermore, we identified large gaps in knowledge when we predicted all cytosolic and mitochondrial human tRNA modification genes. Only 48% of the candidate cytosolic tRNA modification enzymes have been experimentally validated in mammals (either directly or in a heterologous system). Approximately 23% of the modification genes (cytosolic and mitochondrial combined) remain unknown. We discuss these 'unidentified enzymes' cases in detail and propose candidates whenever possible. Finally, tissue-specific expression analysis shows that modification genes are highly expressed in proliferative tissues like testis and transformed cells, but scarcely in differentiated tissues, with the exception of the cerebellum. Our work provides a comprehensive up to date compilation of human tRNA modifications and their enzymes that can be used as a resource for further studies.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA
- Cancer and Genetic Institute, University of Florida, Gainesville, FL 32611, USA
| | - Pietro Boccaletto
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland
| | - Carl G Mangleburg
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Puneet Sharma
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
- Research Group for RNA Biochemistry, Institute of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznań, Poland
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90
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On-line trapping/capillary hydrophilic-interaction liquid chromatography/mass spectrometry for sensitive determination of RNA modifications from human blood. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2018.11.029] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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91
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Miller KN, Clark JP, Anderson RM. Mitochondrial regulator PGC-1a-Modulating the modulator. ACTA ACUST UNITED AC 2019; 5:37-44. [PMID: 31406949 DOI: 10.1016/j.coemr.2019.02.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1a) is a central regulator of metabolism that is poised at the intersection of myriad intracellular signaling pathways. In this brief update, we discuss regulation of PGC-1a at multiple levels, including transcriptional, post-transcriptional, and post-translational modifications. We discuss recently identified small molecule effectors of PGC-1a that offer translational potential and promise new insight into PGC-1a biology. We highlight novel mechanistic insights relating to PGC-1a's interactions with RNA to enhance transcription and potentially influence transcript processing. Finally, we place these exciting new data in the context of aging biology, offering PGC-1a as a candidate target with terrific potential in anti-aging interventions.
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Affiliation(s)
- Karl N Miller
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Josef P Clark
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, USA
| | - Rozalyn M Anderson
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, USA.,GRECC, William S. Middleton Memorial Veterans Hospital, Madison WI, USA
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92
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Bohnsack KE, Höbartner C, Bohnsack MT. Eukaryotic 5-methylcytosine (m⁵C) RNA Methyltransferases: Mechanisms, Cellular Functions, and Links to Disease. Genes (Basel) 2019; 10:genes10020102. [PMID: 30704115 PMCID: PMC6409601 DOI: 10.3390/genes10020102] [Citation(s) in RCA: 274] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 01/04/2023] Open
Abstract
5-methylcytosine (m⁵C) is an abundant RNA modification that's presence is reported in a wide variety of RNA species, including cytoplasmic and mitochondrial ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), as well as messenger RNAs (mRNAs), enhancer RNAs (eRNAs) and a number of non-coding RNAs. In eukaryotes, C5 methylation of RNA cytosines is catalyzed by enzymes of the NOL1/NOP2/SUN domain (NSUN) family, as well as the DNA methyltransferase homologue DNMT2. In recent years, substrate RNAs and modification target nucleotides for each of these methyltransferases have been identified, and structural and biochemical analyses have provided the first insights into how each of these enzymes achieves target specificity. Functional characterizations of these proteins and the modifications they install have revealed important roles in diverse aspects of both mitochondrial and nuclear gene expression. Importantly, this knowledge has enabled a better understanding of the molecular basis of a number of diseases caused by mutations in the genes encoding m⁵C methyltransferases or changes in the expression level of these enzymes.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany.
| | - Claudia Höbartner
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany.
- Göttingen Centre for Molecular Biosciences, University of Göttingen, Göttingen, Justus-von-Liebig-Weg 11, 37077 Germany.
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93
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García-Vílchez R, Sevilla A, Blanco S. Post-transcriptional regulation by cytosine-5 methylation of RNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:240-252. [PMID: 30593929 DOI: 10.1016/j.bbagrm.2018.12.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/04/2018] [Accepted: 12/07/2018] [Indexed: 02/02/2023]
Abstract
The recent advent of high-throughput sequencing technologies coupled with RNA modifications detection methods has allowed the detection of RNA modifications at single nucleotide resolution giving a more comprehensive landscape of post-transcriptional gene regulation pathways. In this review, we focus on the occurrence of 5-methylcytosine (m5C) in the transcriptome. We summarise the main findings of the molecular role in post-transcriptional regulation that governs m5C deposition in RNAs. Functionally, m5C deposition can regulate several cellular and physiological processes including development, differentiation and survival to stress stimuli. Despite many aspects concerning m5C deposition in RNA, such as position or sequence context and the fact that many readers and erasers still remain elusive, the overall recent findings indicate that RNA cytosine methylation is a powerful mechanism to post-transcriptionally regulate physiological processes. In addition, mutations in RNA cytosine-5 methyltransferases are associated to pathological processes ranging from neurological syndromes to cancer.
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Affiliation(s)
| | - Ana Sevilla
- Physiology, Cellular Biology and Immunology Department - Biology Faculty. University of Barcelona, Avda. Diagonal 643, 08028 Barcelona. Spain
| | - Sandra Blanco
- CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain; Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca, 37007 Salamanca, Spain..
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94
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Trixl L, Lusser A. The dynamic RNA modification 5-methylcytosine and its emerging role as an epitranscriptomic mark. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1510. [PMID: 30311405 PMCID: PMC6492194 DOI: 10.1002/wrna.1510] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/30/2018] [Accepted: 09/17/2018] [Indexed: 12/11/2022]
Abstract
It is a well‐known fact that RNA is the target of a plethora of modifications which currently amount to over a hundred. The vast majority of these modifications was observed in the two most abundant classes of RNA, rRNA and tRNA. With the recent advance in mapping technologies, modifications have been discovered also in mRNA and in less abundant non‐coding RNA species. These developments have sparked renewed interest in elucidating the nature and functions of those “epitransciptomic” modifications in RNA. N6‐methyladenosine (m6A) is the best understood and most frequent mark of mRNA with demonstrated functions ranging from pre‐mRNA processing, translation, miRNA biogenesis to mRNA decay. By contrast, much less research has been conducted on 5‐methylcytosine (m5C), which was detected in tRNAs and rRNAs and more recently in poly(A)RNAs. In this review, we discuss recent developments in the discovery of m5C RNA methylomes, the functions of m5C as well as the proteins installing, translating and manipulating this modification. Although our knowledge about m5C in RNA transcripts is just beginning to consolidate, it has become clear that cytosine methylation represents a powerful mechanistic strategy to regulate cellular processes on an epitranscriptomic level. This article is categorized under:RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications RNA Processing > tRNA Processing RNA Turnover and Surveillance > Regulation of RNA Stability
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Affiliation(s)
- Lukas Trixl
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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95
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Biological processes and signal transduction pathways regulated by the protein methyltransferase SETD7 and their significance in cancer. Signal Transduct Target Ther 2018; 3:19. [PMID: 30013796 PMCID: PMC6043541 DOI: 10.1038/s41392-018-0017-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 02/05/2018] [Accepted: 03/21/2018] [Indexed: 02/07/2023] Open
Abstract
Protein methyltransferases have been shown to methylate histone and non-histone proteins, leading to regulation of several biological processes that control cell homeostasis. Over the past few years, the histone-lysine N-methyltransferase SETD7 (SETD7; also known as SET7/9, KIAA1717, KMT7, SET7, SET9) has emerged as an important regulator of at least 30 non-histone proteins and a potential target for the treatment of several human diseases. This review discusses current knowledge of the structure and subcellular localization of SETD7, as well as its function as a histone and non-histone methyltransferase. This work also underlines the putative contribution of SETD7 to the regulation of gene expression, control of cell proliferation, differentiation and endoplasmic reticulum stress, which indicate that SETD7 is a candidate for novel targeted therapies with the aim of either stimulating or inhibiting its activity, depending on the cell signaling context.
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Transcriptional coactivator PGC-1α contains a novel CBP80-binding motif that orchestrates efficient target gene expression. Genes Dev 2018; 32:555-567. [PMID: 29654059 PMCID: PMC5959238 DOI: 10.1101/gad.309773.117] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 03/09/2018] [Indexed: 12/13/2022]
Abstract
In this study, Cho et al. investigated how PGC-1α, a transcriptional coactivator, functions in the metabolic adaptation of mammalian cells to diverse physiological stresses. They used in vitro binding assays, X-ray crystallography, and immunoprecipitations of mouse myoblast cell lysates to define a previously unknown cap-binding protein 80 (CBP80)-binding motif (CBM) in the C terminus of PGC-1α, thus providing insight into a novel cap-binding protein surveillance mechanism. Although peroxisome proliferator-activated receptor-γ (PPARγ) coactivator 1α (PGC-1α) is a well-established transcriptional coactivator for the metabolic adaptation of mammalian cells to diverse physiological stresses, the molecular mechanism by which it functions is incompletely understood. Here we used in vitro binding assays, X-ray crystallography, and immunoprecipitations of mouse myoblast cell lysates to define a previously unknown cap-binding protein 80 (CBP80)-binding motif (CBM) in the C terminus of PGC-1α. We show that the CBM, which consists of a nine-amino-acid α helix, is critical for the association of PGC-1α with CBP80 at the 5′ cap of target transcripts. Results from RNA sequencing demonstrate that the PGC-1α CBM promotes RNA synthesis from promyogenic genes. Our findings reveal a new conduit between DNA-associated and RNA-associated proteins that functions in a cap-binding protein surveillance mechanism, without which efficient differentiation of myoblasts to myotubes fails to occur.
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97
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Sánchez-Vásquez E, Alata Jimenez N, Vázquez NA, Strobl-Mazzulla PH. Emerging role of dynamic RNA modifications during animal development. Mech Dev 2018; 154:24-32. [PMID: 29654887 DOI: 10.1016/j.mod.2018.04.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/07/2018] [Accepted: 04/07/2018] [Indexed: 01/09/2023]
Abstract
The central dogma of molecular biology statically says that the information flows from DNA to messenger RNA to protein. But the recent advances in mass spectrometry and high throughput technology have helped the scientists to view RNA as little more than a courier of genetic information encoded in the DNA. The dynamics of RNA modifications in coding and non-coding RNAs are just emerging as a carrier of non-genetic information, uncovering a new layer of complexity in the regulation of gene expression and protein translation. In this review, we summarize about the current knowledge of N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C) and pseudouridine (Ψ) modifications in RNA, and described how these RNA modifications are implicated in early animal development and in several human diseases.
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Affiliation(s)
- Estefanía Sánchez-Vásquez
- Laboratory of Developmental Biology, Instituto de Investigaciones Biotecnológicas- Instituto Tecnológico de Chascomús (CONICET-UNSAM), Int. Marino 8200, Chascomús 7130, Argentina
| | - Nagif Alata Jimenez
- Laboratory of Developmental Biology, Instituto de Investigaciones Biotecnológicas- Instituto Tecnológico de Chascomús (CONICET-UNSAM), Int. Marino 8200, Chascomús 7130, Argentina
| | - Nicolás A Vázquez
- Laboratory of Developmental Biology, Instituto de Investigaciones Biotecnológicas- Instituto Tecnológico de Chascomús (CONICET-UNSAM), Int. Marino 8200, Chascomús 7130, Argentina
| | - Pablo H Strobl-Mazzulla
- Laboratory of Developmental Biology, Instituto de Investigaciones Biotecnológicas- Instituto Tecnológico de Chascomús (CONICET-UNSAM), Int. Marino 8200, Chascomús 7130, Argentina.
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98
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Gravel SP. Deciphering the Dichotomous Effects of PGC-1α on Tumorigenesis and Metastasis. Front Oncol 2018; 8:75. [PMID: 29629336 PMCID: PMC5876244 DOI: 10.3389/fonc.2018.00075] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/06/2018] [Indexed: 12/31/2022] Open
Abstract
Metabolic reprogramming confers cancer cells the ability to grow and survive under nutrient-depleted or stressful microenvironments. The amplification of oncogenes, the loss of tumor suppressors, as well as context- and lineage-specific determinants can converge and profoundly affect the metabolic status of cancer cells. Cumulating evidences suggest that highly glycolytic cells under the influence of oncogenes such as BRAF, or evolving in hypoxic microenvironments, will promote metastasis through modulation of multiple steps of tumorigenesis such as the epithelial-to-mesenchymal transition (EMT). On the contrary, increased reliance on mitochondrial respiration is associated with hyperplasic rather than metastatic disease. The PGC-1α transcriptional coactivator, a master regulator of mitochondrial biogenesis, has recently been shown to exert antimetastatic effects in cancer, notably through inhibition of EMT. Besides, PGC-1α has the opposite role in specific cancer subtypes, in which it appears to provide growth advantages. Thus, the regulation and role of PGC-1α in cancer is not univocal, and its use as a prognostic marker appears limited given its highly dynamic nature and its multifaceted regulation by transcriptional and posttranslational mechanisms. Herein, we expose key oncogenic and lineage-specific modules that finely regulate PGC-1α to promote or dampen the metastatic process. We propose a unifying model based on the systematic analysis of its controversial implication in cancer from cell proliferation to EMT and metastasis. This short review will provide a good understanding of current challenges associated with the study of PGC-1α.
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Affiliation(s)
- Simon-Pierre Gravel
- Laboratory of Metabolic Immunopharmacology, Faculty of Pharmacy, University of Montreal, Montreal, QC, Canada
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99
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Ding H, Lu WC, Hu JC, Liu YC, Zhang CH, Lian FL, Zhang NX, Meng FW, Luo C, Chen KX. Identification and Characterizations of Novel, Selective Histone Methyltransferase SET7 Inhibitors by Scaffold Hopping- and 2D-Molecular Fingerprint-Based Similarity Search. Molecules 2018; 23:molecules23030567. [PMID: 29498708 PMCID: PMC6017732 DOI: 10.3390/molecules23030567] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 02/23/2018] [Accepted: 02/28/2018] [Indexed: 12/17/2022] Open
Abstract
SET7, serving as the only histone methyltransferase that monomethylates 'Lys-4' of histone H3, has been proved to function as a key regulator in diverse biological processes, such as cell proliferation, transcriptional network regulation in embryonic stem cell, cell cycle control, protein stability, heart morphogenesis and development. What's more, SET7 is involved inthe pathogenesis of alopecia aerate, breast cancer, tumor and cancer progression, atherosclerosis in human carotid plaques, chronic renal diseases, diabetes, obesity, ovarian cancer, prostate cancer, hepatocellular carcinoma, and pulmonary fibrosis. Therefore, there is urgent need to develop novel SET7 inhibitors. In this paper, based on DC-S239 which has been previously reported in our group, we employed scaffold hopping- and 2D fingerprint-based similarity searches and identified DC-S285 as the new hit compound targeting SET7 (IC50 = 9.3 μM). Both radioactive tracing and NMR experiments validated the interactions between DC-S285 and SET7 followed by the second-round similarity search leading to the identification ofDC-S303 with the IC50 value of 1.1 μM. In cellular level, DC-S285 retarded tumor cell proliferation and showed selectivity against MCF7 (IC50 = 21.4 μM), Jurkat (IC50 = 2.2 μM), THP1 (IC50 = 3.5 μM), U937 (IC50 = 3.9 μM) cell lines. Docking calculations suggested that DC-S303 share similar binding mode with the parent compoundDC-S239. What's more, it presented good selectivity against other epigenetic targets, including SETD1B, SETD8, G9a, SMYD2 and EZH2. DC-S303 can serve as a drug-like scaffold which may need further optimization for drug development, and can be used as chemical probe to help the community to better understand the SET7 biology.
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Affiliation(s)
- Hong Ding
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China.
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Wen Chao Lu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Jun Chi Hu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Yu-Chih Liu
- Shanghai ChemPartner Co., Ltd., #5 Building, 998 Halei Road, Shanghai 201203, China.
| | - Chen Hua Zhang
- Shanghai ChemPartner Co., Ltd., #5 Building, 998 Halei Road, Shanghai 201203, China.
| | - Fu Lin Lian
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Nai Xia Zhang
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Fan Wang Meng
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada.
| | - Cheng Luo
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Kai Xian Chen
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China.
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
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