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Xia Y, Chen K, Yang Q, Chen Z, Jin L, Zhang L, Yu X, Wang L, Xie C, Zhao Y, Shen Y, Tong J. Methylation in cornea and corneal diseases: a systematic review. Cell Death Discov 2024; 10:169. [PMID: 38589350 PMCID: PMC11002037 DOI: 10.1038/s41420-024-01935-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/10/2024] Open
Abstract
Corneal diseases are among the primary causes of blindness and vision loss worldwide. However, the pathogenesis of corneal diseases remains elusive, and diagnostic and therapeutic tools are limited. Thus, identifying new targets for the diagnosis and treatment of corneal diseases has gained great interest. Methylation, a type of epigenetic modification, modulates various cellular processes at both nucleic acid and protein levels. Growing evidence shows that methylation is a key regulator in the pathogenesis of corneal diseases, including inflammation, fibrosis, and neovascularization, making it an attractive potential therapeutic target. In this review, we discuss the major alterations of methylation and demethylation at the DNA, RNA, and protein levels in corneal diseases and how these dynamics contribute to the pathogenesis of corneal diseases. Also, we provide insights into identifying potential biomarkers of methylation that may improve the diagnosis and treatment of corneal diseases.
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Affiliation(s)
- Yutong Xia
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Kuangqi Chen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Qianjie Yang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Zhitong Chen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Le Jin
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Liyue Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Xin Yu
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Liyin Wang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Chen Xie
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Yuan Zhao
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Ye Shen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China.
| | - Jianping Tong
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China.
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2
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Moore DS. On the evolution of epigenetics via exaptation: A developmental systems perspective. Ann N Y Acad Sci 2023; 1529:21-32. [PMID: 37750405 DOI: 10.1111/nyas.15065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Evolution and development are interrelated processes influenced by genomic, epigenetic, and environmental factors. Epigenetic processes serve critical roles in development and operate as intermediaries that connect the genome to the rest of the world. Therefore, it is of interest to consider the evolution of epigenetic processes. The developmental systems perspective offers a distinctive, coherent, integrative way to understand the relationships between evolution, epigenetics, development, and the effects of experienced contexts. By adopting this perspective, this paper draws attention to the role of exaptation in the evolution of epigenetics in the RNA world and addresses the role of epigenetics in the later evolution of developmental processes such as cellular differentiation, learning, and memory. In so doing, the paper considers the appearance and functions of epigenetics in evolutionary history-sketching a pathway by which epigenetic processes might have evolved via exaptation and then contributed to the later development and evolution of phenotypes.
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Affiliation(s)
- David S Moore
- Psychology Field Group, Pitzer College, Claremont, California, USA
- Division of Behavioral & Organizational Sciences, Claremont Graduate University, Claremont, California, USA
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3
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Schulz NKE, Mohamed FF, Lo LK, Peuß R, de Buhr MF, Kurtz J. Paternal knockdown of tRNA(cytosine-5-)-methyltransferase (Dnmt2) increases offspring susceptibility to infection in red flour beetles. INSECT MOLECULAR BIOLOGY 2022; 31:711-721. [PMID: 35790040 DOI: 10.1111/imb.12798] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Intergenerational effects from fathers to offspring are increasingly reported from diverse organisms, but the underlying mechanisms remain speculative. Paternal trans-generational immune priming (TGIP) was demonstrated in the red flour beetle Tribolium castaneum: non-infectious bacterial exposure of fathers protects their offspring against an infectious challenge for at least two generations. Epigenetic processes, such as cytosine methylation of nucleic acids, have been proposed to enable transfer of information from fathers to offspring. Here we studied a potential role in TGIP of the Dnmt2 gene (renamed as Trdmt1 in humans), which encodes a highly conserved enzyme that methylates different RNAs, including specific cytosines of a set of tRNAs. Dnmt2 has previously been reported to be involved in intergenerational epigenetic inheritance in mice and protection against viruses in fruit flies. We first studied gene expression and found that Dnmt2 is expressed in various life history stages and tissues of T. castaneum, with high expression in the reproductive organs. RNAi-mediated knockdown of Dnmt2 in fathers was systemic, slowed down offspring larval development and increased mortality of the adult offspring upon bacterial infection. However, these effects were independent of bacterial exposure of the fathers. In conclusion, our results point towards a role of Dnmt2 for paternal effects, while elucidation of the mechanisms behind paternal TGIP needs further studies.
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Affiliation(s)
- Nora K E Schulz
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Fakry F Mohamed
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Institute of Virology Muenster, Center for Molecular Biology of Inflammation (ZMBE), University Hospital Muenster, Muenster, Germany
| | - Lai Ka Lo
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Robert Peuß
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Maike F de Buhr
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Joachim Kurtz
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
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4
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Cheung JCT, Deng G, Wong N, Dong Y, Ng SSM. More than a duologue: In-depth insights into epitranscriptomics and ferroptosis. Front Cell Dev Biol 2022; 10:982606. [PMID: 36172270 PMCID: PMC9511216 DOI: 10.3389/fcell.2022.982606] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/22/2022] [Indexed: 12/02/2022] Open
Abstract
Beyond transcription, RNA molecules are enzymatically modified to influence the biological functions of living organisms. The term “epitranscriptomics” describes the changes in RNA strands aside from altering the innate sequences. Modifications on adenosine (A) are the most widely characterized epitranscriptomic modification, including N6-methyladenosine (m6A), N1-methyladenosine (m1A), polyadenylation, and adenosine-to-inosine (A-to-I) RNA editing, and modifications on other nucleotides seem to be fewer, such as N7-methylguanosine (m7G), 5-methylcytosine (m5C), and pseudouridine (Ψ). These changes on the RNA strand surface, exclusively by their RNA-modifying proteins (RMPs), are reported in various biological phenomena, including programmed cell death (PCD). One necro-biological phenomenon that has been observed for long but has started to gain heed in recent years is “ferroptosis.” The phospholipid peroxidation by polyunsaturated-fatty-acid-containing-phospholipid hydroperoxyl (PLOOH) radicals destroys membrane integrity due to a series of mechanisms. The Fenton reaction, constituting the final Haber–Weiss reaction that is less recognized, collaboratively leading to the conversion of polyunsaturated fatty acid (PUFA) to PLOOH, is the etymological origin of ferroptosis. However, it is with increasing evidence that ferroptotic signaling is also intervened by epitranscriptomic modifications, although the truth is still ambiguous. We attempted to delineate some up-to-date discoveries on both epitranscriptomics and ferroptosis, bringing up the fundamentals to address any potential connection between the two. Next, we discussed whether a duologal relationship, or more, exists between the two, taking the ROS level and iron status into consideration. Lastly, we surveyed future perspectives that would favor the understanding of these topics.
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Affiliation(s)
- Justin Chak Ting Cheung
- Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Guangzheng Deng
- Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Nathalie Wong
- Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yujuan Dong
- Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- *Correspondence: Simon Siu Man Ng, ; Yujuan Dong,
| | - Simon Siu Man Ng
- Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- *Correspondence: Simon Siu Man Ng, ; Yujuan Dong,
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5
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DNA Methyltransferases: From Evolution to Clinical Applications. Int J Mol Sci 2022; 23:ijms23168994. [PMID: 36012258 PMCID: PMC9409253 DOI: 10.3390/ijms23168994] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is an epigenetic mark that living beings have used in different environments. The MTases family catalyzes DNA methylation. This process is conserved from archaea to eukaryotes, from fertilization to every stage of development, and from the early stages of cancer to metastasis. The family of DNMTs has been classified into DNMT1, DNMT2, and DNMT3. Each DNMT has been duplicated or deleted, having consequences on DNMT structure and cellular function, resulting in a conserved evolutionary reaction of DNA methylation. DNMTs are conserved in the five kingdoms of life: bacteria, protists, fungi, plants, and animals. The importance of DNMTs in whether methylate or not has a historical adaptation that in mammals has been discovered in complex regulatory mechanisms to develop another padlock to genomic insurance stability. The regulatory mechanisms that control DNMTs expression are involved in a diversity of cell phenotypes and are associated with pathologies transcription deregulation. This work focused on DNA methyltransferases, their biology, functions, and new inhibitory mechanisms reported. We also discuss different approaches to inhibit DNMTs, the use of non-coding RNAs and nucleoside chemical compounds in recent studies, and their importance in biological, clinical, and industry research.
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m 6A Demethylase ALKBH5 Restrains PEDV Infection by Regulating GAS6 Expression in Porcine Alveolar Macrophages. Int J Mol Sci 2022; 23:ijms23116191. [PMID: 35682869 PMCID: PMC9181496 DOI: 10.3390/ijms23116191] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/22/2022] [Accepted: 05/27/2022] [Indexed: 02/05/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is a burdensome coronavirus for the global pig industry. Although its fecal-oral route has been well-recognized, increasing evidence suggests that PEDV can also spread through airborne routes, indicating that the infection may also occur in the respiratory tract. N6-methyladenosine (m6A) has been known to regulate viral replication and host immunity, yet its regulatory role and molecular mechanism regarding PEDV infection outside the gastrointestinal tract remain unexplored. In this study, we demonstrate that PEDV can infect porcine lung tissue and the 3D4/21 alveolar macrophage cell line, and the key m6A demethylase ALKBH5 is remarkably induced after PEDV infection. Interestingly, the disruption of ALKBH5 expression remarkably increases the infection’s capacity for PEDV. Transcriptome profiling identified dozens of putative targets of ALKBH5, including GAS6, which is known to regulate virus infectivity. Further, MeRIP-qPCR and mRNA stability analyses suggest that ALKBH5 regulates the expression of GAS6 via an m6A-YTHDF2-dependent mechanism. Overall, our study demonstrates that PEDV can infect porcine lung tissue and 3D4/21 cells and reveals the crucial role of ALKBH5 in restraining PEDV infections, at least partly, by influencing GAS6 through an m6A-YTHDF2-dependent mechanism.
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Lateef OM, Akintubosun MO, Olaoba OT, Samson SO, Adamczyk M. Making Sense of "Nonsense" and More: Challenges and Opportunities in the Genetic Code Expansion, in the World of tRNA Modifications. Int J Mol Sci 2022; 23:938. [PMID: 35055121 PMCID: PMC8779196 DOI: 10.3390/ijms23020938] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 01/09/2023] Open
Abstract
The evolutional development of the RNA translation process that leads to protein synthesis based on naturally occurring amino acids has its continuation via synthetic biology, the so-called rational bioengineering. Genetic code expansion (GCE) explores beyond the natural translational processes to further enhance the structural properties and augment the functionality of a wide range of proteins. Prokaryotic and eukaryotic ribosomal machinery have been proven to accept engineered tRNAs from orthogonal organisms to efficiently incorporate noncanonical amino acids (ncAAs) with rationally designed side chains. These side chains can be reactive or functional groups, which can be extensively utilized in biochemical, biophysical, and cellular studies. Genetic code extension offers the contingency of introducing more than one ncAA into protein through frameshift suppression, multi-site-specific incorporation of ncAAs, thereby increasing the vast number of possible applications. However, different mediating factors reduce the yield and efficiency of ncAA incorporation into synthetic proteins. In this review, we comment on the recent advancements in genetic code expansion to signify the relevance of systems biology in improving ncAA incorporation efficiency. We discuss the emerging impact of tRNA modifications and metabolism in protein design. We also provide examples of the latest successful accomplishments in synthetic protein therapeutics and show how codon expansion has been employed in various scientific and biotechnological applications.
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Affiliation(s)
- Olubodun Michael Lateef
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| | | | - Olamide Tosin Olaoba
- Laboratory of Functional and Structural Biochemistry, Federal University of Sao Carlos, Sao Carlos 13565-905, SP, Brazil;
| | - Sunday Ocholi Samson
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| | - Malgorzata Adamczyk
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
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8
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Hutinet G, Lee YJ, de Crécy-Lagard V, Weigele PR. Hypermodified DNA in Viruses of E. coli and Salmonella. EcoSal Plus 2021; 9:eESP00282019. [PMID: 34910575 PMCID: PMC11163837 DOI: 10.1128/ecosalplus.esp-0028-2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/26/2021] [Indexed: 12/23/2022]
Abstract
The DNA in bacterial viruses collectively contains a rich, yet relatively underexplored, chemical diversity of nucleobases beyond the canonical adenine, guanine, cytosine, and thymine. Herein, we review what is known about the genetic and biochemical basis for the biosynthesis of complex DNA modifications, also called DNA hypermodifications, in the DNA of tailed bacteriophages infecting Escherichia coli and Salmonella enterica. These modifications, and their diversification, likely arose out of the evolutionary arms race between bacteriophages and their cellular hosts. Despite their apparent diversity in chemical structure, the syntheses of various hypermodified bases share some common themes. Hypermodifications form through virus-directed synthesis of noncanonical deoxyribonucleotide triphosphates, direct modification DNA, or a combination of both. Hypermodification enzymes are often encoded in modular operons reminiscent of biosynthetic gene clusters observed in natural product biosynthesis. The study of phage-hypermodified DNA provides an exciting opportunity to expand what is known about the enzyme-catalyzed chemistry of nucleic acids and will yield new tools for the manipulation and interrogation of DNA.
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Affiliation(s)
- Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, Massachusetts, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Peter R. Weigele
- Research Department, New England Biolabs, Ipswich, Massachusetts, USA
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9
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Gameiro PA, Encheva V, Dos Santos MS, MacRae JI, Ule J. Metabolic turnover and dynamics of modified ribonucleosides by 13C labeling. J Biol Chem 2021; 297:101294. [PMID: 34634303 PMCID: PMC8567201 DOI: 10.1016/j.jbc.2021.101294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 01/27/2023] Open
Abstract
Tandem mass spectrometry (MS/MS) is an accurate tool to assess modified ribonucleosides and their dynamics in mammalian cells. However, MS/MS quantification of lowly abundant modifications in non-ribosomal RNAs is unreliable, and the dynamic features of various modifications are poorly understood. Here, we developed a 13C labeling approach, called 13C-dynamods, to quantify the turnover of base modifications in newly transcribed RNA. This turnover-based approach helped to resolve mRNA from ncRNA modifications in purified RNA or free ribonucleoside samples and showed the distinct kinetics of the N6-methyladenosine (m6A) versus 7-methylguanosine (m7G) modification in polyA+-purified RNA. We uncovered that N6,N6-dimethyladenosine (m62A) exhibits distinct turnover in small RNAs and free ribonucleosides when compared to known m62A-modified large rRNAs. Finally, combined measurements of turnover and abundance of these modifications informed on the transcriptional versus posttranscriptional sensitivity of modified ncRNAs and mRNAs, respectively, to stress conditions. Thus, 13C-dynamods enables studies of the origin of modified RNAs at steady-state and subsequent dynamics under nonstationary conditions. These results open new directions to probe the presence and biological regulation of modifications in particular RNAs.
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Affiliation(s)
- Paulo A Gameiro
- RNA Networks Laboratory, Francis Crick Institute, London, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK.
| | - Vesela Encheva
- Mass Spectrometry Science Technology Platform, Francis Crick Institute, London, UK
| | | | - James I MacRae
- Mass Spectrometry Science Technology Platform, Francis Crick Institute, London, UK
| | - Jernej Ule
- RNA Networks Laboratory, Francis Crick Institute, London, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
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10
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Ferron F, Sama B, Decroly E, Canard B. The enzymes for genome size increase and maintenance of large (+)RNA viruses. Trends Biochem Sci 2021; 46:866-877. [PMID: 34172362 DOI: 10.1016/j.tibs.2021.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/05/2021] [Accepted: 05/18/2021] [Indexed: 02/08/2023]
Abstract
With sizes <50 kb, viral RNA genomes are at the crossroads of genetic, biophysical, and biochemical stability in their host cell. Here, we analyze the enzymatic assets accompanying large RNA genome viruses, mostly based on recent scientific advances in Coronaviridae. We argue that, in addition to the presence of an RNA exonuclease (ExoN), two markers for the large size of viral RNA genomes are (i) the presence of one or more RNA methyltransferases (MTases) and (ii) a specific architecture of the RNA-dependent RNA polymerase active site. We propose that RNA genome expansion and maintenance are driven by an evolutionary ménage-à-trois made of fast and processive RNA polymerases, RNA repair ExoNs, and RNA MTases that relates to the transition between RNA- to DNA-based life.
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Affiliation(s)
- François Ferron
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, Case 925, 163, Avenue de Luminy, 13009 Marseille, France; European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Bhawna Sama
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, Case 925, 163, Avenue de Luminy, 13009 Marseille, France
| | - Etienne Decroly
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, Case 925, 163, Avenue de Luminy, 13009 Marseille, France
| | - Bruno Canard
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, Case 925, 163, Avenue de Luminy, 13009 Marseille, France; European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany.
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11
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Gao Y, Wang X, Li S, Zhang Z, Li X, Lin F. Identification of a DNA Methylation-Based Prognostic Signature for Patients with Triple-Negative Breast Cancer. Med Sci Monit 2021; 27:e930025. [PMID: 34003815 PMCID: PMC8140526 DOI: 10.12659/msm.930025] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Aberrant DNA methylation is an important biological regulatory mechanism in malignant tumors. However, it remains underutilized for establishing prognostic models for triple-negative breast cancer (TNBC). MATERIAL AND METHODS Methylation data and expression data downloaded from The Cancer Genome Atlas (TCGA) were used to identify differentially methylated sites (DMSs). The prognosis-related DMSs were selected by univariate Cox regression analysis. Functional enrichment was analyzed using DAVID. A protein-protein interaction (PPI) network was constructed using STRING. Finally, a methylation-based prognostic signature was constructed using LASSO method and further validated in 2 validation cohorts. RESULTS Firstly, we identified 743 DMSs corresponding to 332 genes, including 357 hypermethylated sites and 386 hypomethylated sites. Furthermore, we selected 103 prognosis-related DMSs by univariate Cox regression. Using a LASSO algorithm, we established a 5-DMSs prognostic signature in TCGA-TNBC cohort, which could classify TNBC patients with significant survival difference (log-rank p=4.97E-03). Patients in the high-risk group had shorter overall survival than patients in the low-risk group. The excellent performance was validated in GSE78754 (HR=2.42, 95%CI: 1.27-4.59, log-rank P=0.0055). Moreover, for disease-free survival, the prognostic performance was verified in GSE141441 (HR=2.09, 95%CI: 1.28-3.44, log-rank P=0.0027). Multivariate Cox regression analysis indicated that the 5-DMSs signature could serve as an independent risk factor. CONCLUSIONS We constructed a 5-DMSs signature with excellent performance for the prediction of disease-free survival and overall survival, providing a guide for clinicians in directing personalized therapeutic regimen selection of TNBC patients.
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Affiliation(s)
- Yinqi Gao
- Department of Breast Surgery, Capital Medical University Electric Power Teaching Hospital, Beijing, China (mainland)
| | - Xuelong Wang
- Department of Thoracic Surgery, Capital Medical University Electric Power Teaching Hospital, Beijing, China (mainland)
| | - Shihui Li
- Department of Breast Surgery, Capital Medical University Electric Power Teaching Hospital, Beijing, China (mainland)
| | - Zhiqiang Zhang
- Department of Breast Surgery, Capital Medical University Electric Power Teaching Hospital, Beijing, China (mainland)
| | - Xuefei Li
- Department of Breast Surgery, Capital Medical University Electric Power Teaching Hospital, Beijing, China (mainland)
| | - Fangcai Lin
- Department of Breast Surgery, Capital Medical University Electric Power Teaching Hospital, Beijing, China (mainland)
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12
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Gerrits L, Hammink R, Kouwer PHJ. Semiflexible polymer scaffolds: an overview of conjugation strategies. Polym Chem 2021. [DOI: 10.1039/d0py01662d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Semiflexible polymers are excellent scaffolds for the presentation of a wide variety of (bio)molecules. This manuscript reviews advantages and challenges of the most common conjugation strategies for the major classes of semiflexible polymers.
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Affiliation(s)
- Lotte Gerrits
- Institute for Molecules and Materials
- Radboud University
- 6525 AJ Nijmegen
- The Netherlands
| | - Roel Hammink
- Department of Tumor Immunology
- Radboud Institute for Molecular Life Sciences
- Radboud University Medical Center
- 6525 GA Nijmegen
- The Netherlands
| | - Paul H. J. Kouwer
- Institute for Molecules and Materials
- Radboud University
- 6525 AJ Nijmegen
- The Netherlands
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13
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Peng Y, Shui L, Xie J, Liu S. Development and validation of a novel 15-CpG-based signature for predicting prognosis in triple-negative breast cancer. J Cell Mol Med 2020; 24:9378-9387. [PMID: 32649035 PMCID: PMC7417707 DOI: 10.1111/jcmm.15588] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/05/2020] [Accepted: 06/07/2020] [Indexed: 02/05/2023] Open
Abstract
DNA methylation is an important biological regulatory mechanism that changes gene expression without altering the DNA sequence. Increasing studies have revealed that DNA methylation data play a vital role in the field of oncology. However, the methylation site signature in triple‐negative breast cancer (TNBC) remains unknown. In our research, we analysed 158 TNBC samples and 98 noncancerous samples from The Cancer Genome Atlas (TCGA) in three phases. In the discovery phase, 86 CpGs were identified by univariate Cox proportional hazards regression (CPHR) analyses to be significantly correlated with overall survival (P < 0.01). In the training phase, these candidate CpGs were further narrowed down to a 15‐CpG‐based signature by conducting least absolute shrinkage and selector operator (LASSO) Cox regression in the training set. In the validation phase, the 15‐CpG‐based signature was verified using two different internal sets and one external validation set. Furthermore, a nomogram comprising the CpG‐based signature and TNM stage was generated to predict the 1‐, 3‐ and 5‐year overall survival in the primary set, and it showed excellent performance in the three validation sets (concordance indexes: 0.924, 0.974 and 0.637). This study showed that our nomogram has a precise predictive effect on the prognosis of TNBC and can potentially be implemented for clinical treatment and diagnosis.
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Affiliation(s)
- Yang Peng
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lin Shui
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jian Xie
- Department of General Surgery, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Shengchun Liu
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Fustin JM, Ye S, Rakers C, Kaneko K, Fukumoto K, Yamano M, Versteven M, Grünewald E, Cargill SJ, Tamai TK, Xu Y, Jabbur ML, Kojima R, Lamberti ML, Yoshioka-Kobayashi K, Whitmore D, Tammam S, Howell PL, Kageyama R, Matsuo T, Stanewsky R, Golombek DA, Johnson CH, Kakeya H, van Ooijen G, Okamura H. Methylation deficiency disrupts biological rhythms from bacteria to humans. Commun Biol 2020; 3:211. [PMID: 32376902 PMCID: PMC7203018 DOI: 10.1038/s42003-020-0942-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 04/03/2020] [Indexed: 12/20/2022] Open
Abstract
The methyl cycle is a universal metabolic pathway providing methyl groups for the methylation of nuclei acids and proteins, regulating all aspects of cellular physiology. We have previously shown that methyl cycle inhibition in mammals strongly affects circadian rhythms. Since the methyl cycle and circadian clocks have evolved early during evolution and operate in organisms across the tree of life, we sought to determine whether the link between the two is also conserved. Here, we show that methyl cycle inhibition affects biological rhythms in species ranging from unicellular algae to humans, separated by more than 1 billion years of evolution. In contrast, the cyanobacterial clock is resistant to methyl cycle inhibition, although we demonstrate that methylations themselves regulate circadian rhythms in this organism. Mammalian cells with a rewired bacteria-like methyl cycle are protected, like cyanobacteria, from methyl cycle inhibition, providing interesting new possibilities for the treatment of methylation deficiencies. Fustin et al. reveal the evolutionarily conserved link between methyl metabolism and biological clocks. This study suggests the possibility of translating fundamental understanding of methylation deficiencies to clinical applications.
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Affiliation(s)
- Jean-Michel Fustin
- Graduate School of Pharmaceutical Sciences, Laboratory of Molecular Metabology, Kyoto University, Kyoto, Japan. .,The University of Manchester, Faculty of Biology, Medicine and Health, Oxford Road, Manchester, M13 9PL, UK.
| | - Shiqi Ye
- Graduate School of Pharmaceutical Sciences, Laboratory of Molecular Metabology, Kyoto University, Kyoto, Japan
| | - Christin Rakers
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Kensuke Kaneko
- Graduate School of Pharmaceutical Sciences, Department of System Chemotherapy and Molecular Sciences, Kyoto University, Kyoto, Japan
| | - Kazuki Fukumoto
- Graduate School of Pharmaceutical Sciences, Laboratory of Molecular Metabology, Kyoto University, Kyoto, Japan
| | - Mayu Yamano
- Graduate School of Pharmaceutical Sciences, Laboratory of Molecular Metabology, Kyoto University, Kyoto, Japan
| | - Marijke Versteven
- Institute of Neuro- and Behavioral Biology, University of Münster, Münster, Germany
| | - Ellen Grünewald
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - T Katherine Tamai
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yao Xu
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Maria Luísa Jabbur
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | | | - Melisa L Lamberti
- Department of Science and Technology, National University of Quilmes/CONICET, Buenos Aires, Argentina
| | | | - David Whitmore
- Centre for Cell and Molecular Dynamics, Department of Cell and Developmental Biology, University College London, London, UK
| | - Stephanie Tammam
- Molecular Medicine, Peter Gilgan Centre for Research and Learning (PGCRL), The Hospital for Sick Children, Toronto, ON, Canada
| | - P Lynne Howell
- Molecular Medicine, Peter Gilgan Centre for Research and Learning (PGCRL), The Hospital for Sick Children, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Ryoichiro Kageyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Takuya Matsuo
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Ralf Stanewsky
- Institute of Neuro- and Behavioral Biology, University of Münster, Münster, Germany
| | - Diego A Golombek
- Department of Science and Technology, National University of Quilmes/CONICET, Buenos Aires, Argentina
| | | | - Hideaki Kakeya
- Graduate School of Pharmaceutical Sciences, Department of System Chemotherapy and Molecular Sciences, Kyoto University, Kyoto, Japan
| | - Gerben van Ooijen
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Hitoshi Okamura
- Graduate School of Pharmaceutical Sciences, Laboratory of Molecular Brain Science, Kyoto University, Kyoto, Japan. .,Kyoto University, Graduate School of Medicine, Department of Neuroscience, Division of Physiology and Neurobiology, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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15
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Hypermethylation of tumor necrosis factor decoy receptor gene in non-small cell lung cancer. Oncol Lett 2020; 20:155-164. [PMID: 32565943 PMCID: PMC7286129 DOI: 10.3892/ol.2020.11565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 03/06/2020] [Indexed: 01/16/2023] Open
Abstract
Abnormal methylation of the TNFRSF10C and TNFRSF10D genes has been observed in numerous types of cancer; however, no studies have investigated the methylation of these genes in non-small cell lung cancer (NSCLC). The aim of the present study was to investigate the association between TNFRSF10C and TNFRSF10D methylation and NSCLC. Methylation levels of 44 pairs of NSCLC tumor tissues and distant non-tumor tissues were analyzed using quantitative methylation specific PCR and methylation reference percentage values (PMR). The methylation levels of the TNFRSF10C gene in NSCLC tumor tissue samples were significantly higher compared with those in the distant non-tumor tissues (median PMR, 2.73% vs. 0.75%; P=0.013). Subgroup analysis demonstrated that the methylation levels of TNFRSF10C in tumor tissues from male patients were significantly higher compared with those in distant non-tumor tissues (median PMR, 2.73% vs. 0.75%; P=0.041). The levels of TNFRSF10C methylation were also higher in the tumor tissues of patients who were non-smokers compared with their distant non-tumor tissues (median PMR, 2.50% vs. 0.63%; P=0.013). TNFRSF10C methylation levels were higher in the tumor tissues from male patients compared with those from female patients (median PMR, 2.50% vs. 0.63%; P=0.031). However, no significant differences in the methylation levels of the TNFRSF10D gene were observed between the sexes. Using the cBioPortal and The Cancer Genome Atlas lung cancer data, it was demonstrated that TNFRSF10C methylation levels were inversely correlated with TNFRSF10C mRNA expression levels (r=-0.379; P=0.008). In addition, demethylation of lung cancer cell lines A549 and NCI-H1299 using 5'-aza-deoxycytidine further confirmed that TNFRSF10C hypomethylation was associated with significant upregulation of TNFRSF10C mRNA expression levels [A549 fold-change (FC)=8; P=1.0×10-4; NCI-H1299 FC=3.163; P=1.143×10-5]. A dual luciferase reporter gene assay was also performed with the insert of TNFRSF10C promoter region, and the results revealed that the TNFRSF10C gene fragment significantly enhanced the transcriptional activity of the reporter gene compared with that in the control group (FC=1.570; P=0.032). Overall, the results of the present study demonstrated that hypermethylation of TNFRSF10C was associated with NSCLC.
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16
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Ferron F, Debat HJ, Shannon A, Decroly E, Canard B. A N7-guanine RNA cap methyltransferase signature-sequence as a genetic marker of large genome, non-mammalian Tobaniviridae. NAR Genom Bioinform 2019; 2:lqz022. [PMID: 32289120 PMCID: PMC7107822 DOI: 10.1093/nargab/lqz022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/22/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022] Open
Abstract
The order Nidovirales is a diverse group of (+)RNA viruses, classified together based on their common genome organisation and conserved replicative enzymes, despite drastic differences in size and complexity. One such difference pertains to the mechanisms and enzymes responsible for generation of the proposed viral 5′ RNA cap. Within the Coronaviridae family, two separate methytransferases (MTase), nsp14 and nsp16, perform the RNA-cap N7-guanine and 2′-OH methylation respectively for generation of the proposed m7GpppNm type I cap structure. For the majority of other families within the Nidovirales order, the presence, structure and key enzymes involved in 5′ capping are far less clear. These viruses either lack completely an RNA MTase signature sequence, or lack an N7-guanine methyltransferase signature sequence, obscuring our understanding about how RNA-caps are N7-methylated for these families. Here, we report the discovery of a putative Rossmann fold RNA methyltransferase in 10 Tobaniviridae members in Orf1a, an unusual genome locus for this gene. Multiple sequence alignments and structural analyses lead us to propose this novel gene as a typical RNA-cap N7-guanine MTase with substrate specificity and active-site organization similar to the canonical eukaryotic RNA-cap N7-guanine MTase.
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Affiliation(s)
- François Ferron
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France.,European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Humberto J Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, X5119 Córdoba, Argentina
| | - Ashleigh Shannon
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| | - Etienne Decroly
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, Polytech Case 925, 13009 Marseille, France.,European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
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17
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Tao C, Luo R, Song J, Zhang W, Ran L. A seven‐DNA methylation signature as a novel prognostic biomarker in breast cancer. J Cell Biochem 2019; 121:2385-2393. [DOI: 10.1002/jcb.29461] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/08/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Chuntao Tao
- Department of Bioinformatics Chongqing Medical University Chongqing China
| | - Ruihan Luo
- Department of Bioinformatics Chongqing Medical University Chongqing China
| | - Jing Song
- Department of Bioinformatics Chongqing Medical University Chongqing China
| | - Wanfeng Zhang
- Department of Bioinformatics Chongqing Medical University Chongqing China
| | - Longke Ran
- Department of Bioinformatics Chongqing Medical University Chongqing China
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18
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Li J, Yang X, Qi Z, Sang Y, Liu Y, Xu B, Liu W, Xu Z, Deng Y. The role of mRNA m 6A methylation in the nervous system. Cell Biosci 2019; 9:66. [PMID: 31452869 PMCID: PMC6701067 DOI: 10.1186/s13578-019-0330-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/14/2019] [Indexed: 11/21/2022] Open
Abstract
Epitranscriptomics, also known as “RNA epigenetics”, is a chemical modification for RNA regulation. Ribonucleic acid (RNA) methylation is considered to be a major discovery following the deoxyribonucleic acid (DNA) and histone methylation. Messenger RNA (mRNA) methylation modification accounts for more than 60% of all RNA modifications and N6-methyladenosine (m6A) is known as one of the most common type of eukaryotic mRNA methylation modifications in current. The m6A modification is a dynamic reversible modification, which can directly or indirectly affect biological processes, such as RNA degradation, translation and splicing, and can play important biological roles in vivo. This article introduces the mRNA m6A methylation modification enzymes and binding proteins, and reviews the research progress and related mechanisms of the role of mRNA m6A methylation in the nervous system from the aspects of neural stem cells, learning and memory, brain development, axon growth and glioblastoma.
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Affiliation(s)
- Jiashuo Li
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Xinxin Yang
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Zhipeng Qi
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Yanqi Sang
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Yanan Liu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Bin Xu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Wei Liu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Zhaofa Xu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Yu Deng
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
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19
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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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20
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Abbasi IHR, Abbasi F, Wang L, Abd El Hack ME, Swelum AA, Hao R, Yao J, Cao Y. Folate promotes S-adenosyl methionine reactions and the microbial methylation cycle and boosts ruminants production and reproduction. AMB Express 2018; 8:65. [PMID: 29687201 PMCID: PMC5913057 DOI: 10.1186/s13568-018-0592-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 04/13/2018] [Indexed: 12/14/2022] Open
Abstract
Folate has gained significant attention due to its vital role in biological methylation and epigenetic machinery. Folate, or vitamin (B9), is only produced through a de novo mechanism by plants and micro-organisms in the rumen of mature animals. Although limited research has been conducted on folate in ruminants, it has been noted that ruminal synthesis could not maintain folate levels in high yielding dairy animals. Folate has an essential role in one-carbon metabolism and is a strong antiproliferative agent. Folate increases DNA stability, being crucial for DNA synthesis and repair, the methylation cycle, and preventing oxidation of DNA by free radicals. Folate is also critical for cell division, metabolism of proteins, synthesis of purine and pyrimidine, and increasing the de novo delivery of methyl groups and S-adenosylmethionine. However, in ruminants, metabolism of B12 and B9 vitamins are closely connected and utilization of folate by cells is significantly affected by B12 vitamin concentration. Supplementation of folate through diet, particularly in early lactation, enhanced metabolic efficiency, lactational performance, and nutritional quality of milk. Impaired absorption, oxidative degradation, or deficient supply of folate in ruminants affects DNA stability, cell division, homocysteine remethylation to methionine, de novo synthesis of S-adenosylmethionine, and increases DNA hypomethylation, uracil misincorporation into DNA, chromosomal damage, abnormal cell growth, oxidative species, premature birth, low calf weight, placental tube defects, and decreases production and reproduction of ruminant animals. However, more studies are needed to overcome these problems and reduce enormous dietary supplement waste and impaired absorption of folate in ruminants. This review was aimed to highlight the vital role of folic acid in ruminants performance.
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21
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Chen X, Sun YZ, Liu H, Zhang L, Li JQ, Meng J. RNA methylation and diseases: experimental results, databases, Web servers and computational models. Brief Bioinform 2017; 20:896-917. [DOI: 10.1093/bib/bbx142] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/12/2017] [Indexed: 12/15/2022] Open
Affiliation(s)
- Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Ya-Zhou Sun
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Hui Liu
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Lin Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Jian-Qiang Li
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Jia Meng
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University
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22
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Glabonjat RA, Raber G, Jensen KB, Guttenberger N, Zangger K, Francesconi KA. A 2- O
-Methylriboside Unknown Outside the RNA World Contains Arsenic. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ronald A. Glabonjat
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Georg Raber
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Kenneth B. Jensen
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Nikolaus Guttenberger
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Klaus Zangger
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Kevin A. Francesconi
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
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23
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Glabonjat RA, Raber G, Jensen KB, Guttenberger N, Zangger K, Francesconi KA. A 2-O
-Methylriboside Unknown Outside the RNA World Contains Arsenic. Angew Chem Int Ed Engl 2017; 56:11963-11965. [DOI: 10.1002/anie.201706310] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Ronald A. Glabonjat
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Georg Raber
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Kenneth B. Jensen
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Nikolaus Guttenberger
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Klaus Zangger
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Kevin A. Francesconi
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
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24
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Next-Generation Sequencing-Based RiboMethSeq Protocol for Analysis of tRNA 2'-O-Methylation. Biomolecules 2017; 7:biom7010013. [PMID: 28208788 PMCID: PMC5372725 DOI: 10.3390/biom7010013] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 02/02/2017] [Indexed: 12/16/2022] Open
Abstract
Analysis of RNA modifications by traditional physico-chemical approaches is labor intensive, requires substantial amounts of input material and only allows site-by-site measurements. The recent development of qualitative and quantitative approaches based on next-generation sequencing (NGS) opens new perspectives for the analysis of various cellular RNA species. The Illumina sequencing-based RiboMethSeq protocol was initially developed and successfully applied for mapping of ribosomal RNA (rRNA) 2′-O-methylations. This method also gives excellent results in the quantitative analysis of rRNA modifications in different species and under varying growth conditions. However, until now, RiboMethSeq was only employed for rRNA, and the whole sequencing and analysis pipeline was only adapted to this long and rather conserved RNA species. A deep understanding of RNA modification functions requires large and global analysis datasets for other important RNA species, namely for transfer RNAs (tRNAs), which are well known to contain a great variety of functionally-important modified residues. Here, we evaluated the application of the RiboMethSeq protocol for the analysis of tRNA 2′-O-methylation in Escherichia coli and in Saccharomyces cerevisiae. After a careful optimization of the bioinformatic pipeline, RiboMethSeq proved to be suitable for relative quantification of methylation rates for known modified positions in different tRNA species.
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25
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Flavin-Dependent Methylation of RNAs: Complex Chemistry for a Simple Modification. J Mol Biol 2016; 428:4867-4881. [PMID: 27825927 DOI: 10.1016/j.jmb.2016.10.031] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 10/19/2016] [Accepted: 10/31/2016] [Indexed: 12/28/2022]
Abstract
RNA methylation is the most abundant and evolutionarily conserved chemical modification of bases or ribose in noncoding and coding RNAs. This rather simple modification has nevertheless major consequences on the function of maturated RNA molecules and ultimately on their cellular fates. The methyl group employed in the methylation is almost universally derived from S-adenosyl-L-methionine via a simple SN2 displacement reaction. However, in some rare cases, the carbon originates from N5,N10-methylenetetrahydrofolate (CH2=THF). Here, a methylene group is transferred first and requires a subsequent reduction step (2e-+H+) via the flavin adenine dinucleotide hydroquinone (FADH-) to form the final methylated derivative. This FAD/folate-dependent mode of chemical reaction, called reductive methylation, is thus far more complex than the usual simple S-adenosyl-L-methionine-dependent one. This reaction is catalyzed by flavoenzymes, now named TrmFO and RlmFO, which respectively modify transfer and ribosomal RNAs. In this review, we briefly recount how these new RNA methyltransferases were discovered and describe a novel aspect of the chemistry of flavins, wherein this versatile biological cofactor is not just a simple redox catalyst but is also a new methyl transfer agent acting via a critical CH2=(N5)FAD iminium intermediate. The enigmatic structural reorganization of these enzymes that needs to take place during catalysis in order to build their active center is also discussed. Finally, recent findings demonstrated that this flavin-dependent mechanism is also employed by enzymatic systems involved in DNA synthesis, suggesting that the use of this cofactor as a methylating agent of biomolecules could be far more usual than initially anticipated.
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