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Xie NB, Wang M, Ji TT, Guo X, Gang FY, Hao Y, Zeng L, Wang YF, Feng YQ, Yuan BF. Simultaneous detection of 5-methylcytosine and 5-hydroxymethylcytosine at specific genomic loci by engineered deaminase-assisted sequencing. Chem Sci 2024; 15:10073-10083. [PMID: 38966352 PMCID: PMC11220598 DOI: 10.1039/d4sc00930d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/17/2024] [Indexed: 07/06/2024] Open
Abstract
Cytosine modifications, particularly 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), play crucial roles in numerous biological processes. Current analytical methods are often constrained to the separate detection of either 5mC or 5hmC, or the combination of both modifications. The ability to simultaneously detect C, 5mC, and 5hmC at the same genomic locations with precise stoichiometry is highly desirable. Herein, we introduce a method termed engineered deaminase-assisted sequencing (EDA-seq) for the simultaneous quantification of C, 5mC, and 5hmC at the same genomic sites. EDA-seq utilizes a specially engineered protein, derived from human APOBEC3A (A3A), known as eA3A-M5. eA3A-M5 exhibits distinct deamination capabilities for C, 5mC, and 5hmC. In EDA-seq, C undergoes complete deamination and is sequenced as T. 5mC is partially deaminated resulting in a mixed readout of T and C, and 5hmC remains undeaminated and is read as C. Consequently, the proportion of T readouts (P T) reflects the collective occurrences of C and 5mC, regulated by the deamination rate of 5mC (R 5mC). By determining R 5mC and P T values, we can deduce the precise levels of C, 5mC, and 5hmC at particular genomic locations. We successfully used EDA-seq to simultaneously measure C, 5mC, and 5hmC at specific loci within human lung cancer tissue and their normal counterpart. The results from EDA-seq demonstrated a strong concordance with those obtained from the combined application of BS-seq and ACE-seq methods. EDA-seq eliminates the need for bisulfite treatment, DNA oxidation or glycosylation and uniquely enables simultaneous quantification of C, 5mC and 5hmC at the same genomic locations.
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Affiliation(s)
- Neng-Bin Xie
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University Wuhan 430071 China
- Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University Wuhan 430060 China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences Wuhan 430071 China
| | - Min Wang
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 China
- College of Chemical Engineering and Environmental Chemistry, Weifang University Weifang 261061 China
| | - Tong-Tong Ji
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 China
| | - Xia Guo
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 China
| | - Fang-Yin Gang
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University Wuhan 430071 China
| | - Ying Hao
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 China
| | - Li Zeng
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 China
| | - Ya-Fen Wang
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University Wuhan 430071 China
| | - Yu-Qi Feng
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University Wuhan 430071 China
| | - Bi-Feng Yuan
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University Wuhan 430071 China
- Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University Wuhan 430060 China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences Wuhan 430071 China
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 China
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2
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Roy S, Das A, Bairagi A, Das D, Jha A, Srivastava AK, Chatterjee N. Mitochondria act as a key regulatory factor in cancer progression: Current concepts on mutations, mitochondrial dynamics, and therapeutic approach. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 793:108490. [PMID: 38460864 DOI: 10.1016/j.mrrev.2024.108490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 02/12/2024] [Accepted: 02/22/2024] [Indexed: 03/11/2024]
Abstract
The diversified impacts of mitochondrial function vs. dysfunction have been observed in almost all disease conditions including cancers. Mitochondria play crucial roles in cellular homeostasis and integrity, however, mitochondrial dysfunctions influenced by alterations in the mtDNA can disrupt cellular balance. Many external stimuli or cellular defects that cause cellular integrity abnormalities, also impact mitochondrial functions. Imbalances in mitochondrial activity can initiate and lead to accumulations of genetic mutations and can promote the processes of tumorigenesis, progression, and survival. This comprehensive review summarizes epigenetic and genetic alterations that affect the functionality of the mitochondria, with considerations of cellular metabolism, and as influenced by ethnicity. We have also reviewed recent insights regarding mitochondrial dynamics, miRNAs, exosomes that play pivotal roles in cancer promotion, and the impact of mitochondrial dynamics on immune cell mechanisms. The review also summarizes recent therapeutic approaches targeting mitochondria in anti-cancer treatment strategies.
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Affiliation(s)
- Sraddhya Roy
- Chittaranjan National Cancer Institute, 37 S. P. Mukherjee Road, Kolkata 700026, India
| | - Ananya Das
- Chittaranjan National Cancer Institute, 37 S. P. Mukherjee Road, Kolkata 700026, India
| | - Aparajita Bairagi
- Chittaranjan National Cancer Institute, 37 S. P. Mukherjee Road, Kolkata 700026, India
| | - Debangshi Das
- Chittaranjan National Cancer Institute, 37 S. P. Mukherjee Road, Kolkata 700026, India
| | - Ashna Jha
- Chittaranjan National Cancer Institute, 37 S. P. Mukherjee Road, Kolkata 700026, India
| | - Amit Kumar Srivastava
- CSIR-IICB Translational Research Unit Of Excellence, CN-6, Salt Lake, Sector - V, Kolkata 700091, India
| | - Nabanita Chatterjee
- Chittaranjan National Cancer Institute, 37 S. P. Mukherjee Road, Kolkata 700026, India.
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3
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Erlitzki N, Kohli RM. An Overview of Global, Local, and Base-Resolution Methods for the Detection of 5-Hydroxymethylcytosine in Genomic DNA. Methods Mol Biol 2024; 2842:325-352. [PMID: 39012604 DOI: 10.1007/978-1-0716-4051-7_17] [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: 07/17/2024]
Abstract
The discovery of 5-hydroxymethylcytosine (5hmC) as a common DNA modification in mammalian genomes has ushered in new areas of inquiry regarding the dynamic epigenome. The balance between 5hmC and its precursor, 5-methylcytosine (5mC), has emerged as a determinant of key processes including cell fate specification, and alterations involving these bases have been implicated in the pathogenesis of various diseases. The identification of 5hmC separately from 5mC initially posed a challenge given that legacy epigenetic sequencing technologies could not discriminate between these two most abundant modifications, a significant blind spot considering their potentially functionally opposing roles. The growing interest in 5hmC, as well as in the Ten-Eleven Translocation (TET) family enzymes that catalyze its generation and further oxidation to 5-formylcytosine (5fC) and 5-carboxycytosine (5caC), has spurred the development of versatile methods for 5hmC detection. These methods enable the quantification and localization of 5hmC in diverse biological samples and, in some cases, at the resolution of individual nucleotides. However, navigating this growing toolbox of methods for 5hmC detection can be challenging. Here, we detail existing and emerging methods for the detection, quantification, and localization of 5hmC at global, locus-specific, and base resolution levels. These methods are discussed in the context of their advantages and limitations, with the goal of providing a framework to help guide researchers in choosing the level of resolution and the associated method that could be most suitable for specific needs.
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Affiliation(s)
- Noa Erlitzki
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
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4
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Xie NB, Wang M, Chen W, Ji TT, Guo X, Gang FY, Wang YF, Feng YQ, Liang Y, Ci W, Yuan BF. Whole-Genome Sequencing of 5-Hydroxymethylcytosine at Base Resolution by Bisulfite-Free Single-Step Deamination with Engineered Cytosine Deaminase. ACS CENTRAL SCIENCE 2023; 9:2315-2325. [PMID: 38161361 PMCID: PMC10755730 DOI: 10.1021/acscentsci.3c01131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/26/2023] [Accepted: 11/06/2023] [Indexed: 01/03/2024]
Abstract
The epigenetic modification 5-hydroxymethylcytosine (5hmC) plays a crucial role in the regulation of gene expression. Although some methods have been developed to detect 5hmC, direct genome-wide mapping of 5hmC at base resolution is still highly desirable. Herein, we proposed a single-step deamination sequencing (SSD-seq) method, designed to precisely map 5hmC across the genome at single-base resolution. SSD-seq takes advantage of a screened engineered human apolipoprotein B mRNA-editing catalytic polypeptide-like 3A (A3A) protein, known as eA3A-v10, to selectively deaminate cytosine (C) and 5-methylcytosine (5mC) but not 5hmC. During sequencing, the deaminated C and 5mC are converted to uracil (U) and thymine (T), read as T in the sequencing data. However, 5hmC remains unaffected by eA3A-v10 and is read as C during sequencing. Consequently, the presence of C in the sequence reads indicates the original 5hmC. We applied SSD-seq to generate a base-resolution map of 5hmC in human lung tissue. Our findings revealed that 5hmC was predominantly localized to CpG dinucleotides. Furthermore, the base-resolution map of 5hmC generated by SSD-seq demonstrated a strong correlation with prior ACE-seq results. The advantages of SSD-seq are its single-step process, absence of bisulfite treatment or DNA glycosylation, cost effectiveness, and ability to detect and quantify 5hmC directly at single-base resolution.
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Affiliation(s)
- Neng-Bin Xie
- Department
of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan 430071, China
- Research
Center of Public Health, Renmin Hospital
of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Min Wang
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Wei Chen
- Department
of Laboratory Medicine, Zhongnan Hospital
of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Tong-Tong Ji
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Xia Guo
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Fang-Yin Gang
- Department
of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan 430071, China
| | - Ya-Feng Wang
- Department
of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan 430071, China
| | - Yu-Qi Feng
- Department
of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan 430071, China
| | - Yuan Liang
- Key
Laboratory of Genomics and Precision Medicine, and China National
Center for Bioinformation, Beijing Institute
of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Weimin Ci
- Key
Laboratory of Genomics and Precision Medicine, and China National
Center for Bioinformation, Beijing Institute
of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Bi-Feng Yuan
- Department
of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan 430071, China
- Research
Center of Public Health, Renmin Hospital
of Wuhan University, Wuhan University, Wuhan 430060, China
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
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5
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Xie Y, Chan LY, Cheung MY, Li MW, Lam HM. Current technical advancements in plant epitranscriptomic studies. THE PLANT GENOME 2023; 16:e20316. [PMID: 36890704 DOI: 10.1002/tpg2.20316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
The growth and development of plants are the result of the interplay between the internal developmental programming and plant-environment interactions. Gene expression regulations in plants are made up of multi-level networks. In the past few years, many studies were carried out on co- and post-transcriptional RNA modifications, which, together with the RNA community, are collectively known as the "epitranscriptome." The epitranscriptomic machineries were identified and their functional impacts characterized in a broad range of physiological processes in diverse plant species. There is mounting evidence to suggest that the epitranscriptome provides an additional layer in the gene regulatory network for plant development and stress responses. In the present review, we summarized the epitranscriptomic modifications found so far in plants, including chemical modifications, RNA editing, and transcript isoforms. The various approaches to RNA modification detection were described, with special emphasis on the recent development and application potential of third-generation sequencing. The roles of epitranscriptomic changes in gene regulation during plant-environment interactions were discussed in case studies. This review aims to highlight the importance of epitranscriptomics in the study of gene regulatory networks in plants and to encourage multi-omics investigations using the recent technical advancements.
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Affiliation(s)
- Yichun Xie
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Long-Yiu Chan
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ming-Yan Cheung
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Man-Wah Li
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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Ortega-Alarcon D, Claveria-Gimeno R, Vega S, Jorge-Torres OC, Esteller M, Abian O, Velazquez-Campoy A. Unexpected thermodynamic signature for the interaction of hydroxymethylated DNA with MeCP2. Int J Biol Macromol 2023; 232:123373. [PMID: 36702223 DOI: 10.1016/j.ijbiomac.2023.123373] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/24/2023]
Abstract
Hydroxymethylated cytosine (5hmC) is a stable DNA epigenetic mark recognized by methyl-CpG binding protein 2 (MeCP2), which acts as a transcriptional regulator and a global chromatin-remodeling element. Because 5hmC triggers a gene regulation response markedly different from that produced by methylated cytosine (5mC), both modifications must affect DNA structure and/or DNA interaction with MeCP2 differently. MeCP2 is a six-domain intrinsically disordered protein (IDP) with two domains responsible for dsDNA binding: methyl-CpG binding domain (MBD) and intervening domain (ID). Here we report the detailed thermodynamic characterization of the interaction of hmCpG-DNA with MeCP2. We find that hmCpG-DNA interacts with MeCP2 in a distinctly different mode with a particular thermodynamic signature, compared to methylated or unmethylated DNA. In addition, we find evidence for Rett syndrome-associated mutations altering the interaction of MeCP2 with dsDNA in a cytosine modification-specific manner which may correlate with disease onset time and clinical severity score.
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Affiliation(s)
- David Ortega-Alarcon
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units GBsC-CSIC-BIFI and ICVV-CSIC-BIFI, Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Rafael Claveria-Gimeno
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units GBsC-CSIC-BIFI and ICVV-CSIC-BIFI, Universidad de Zaragoza, Zaragoza 50018, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
| | - Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units GBsC-CSIC-BIFI and ICVV-CSIC-BIFI, Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Olga C Jorge-Torres
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), l'Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units GBsC-CSIC-BIFI and ICVV-CSIC-BIFI, Universidad de Zaragoza, Zaragoza 50018, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain.
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units GBsC-CSIC-BIFI and ICVV-CSIC-BIFI, Universidad de Zaragoza, Zaragoza 50018, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain.
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7
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Yu W, Wang HL, Zhang J, Yin C. The effects of epigenetic modifications on bone remodeling in age-related osteoporosis. Connect Tissue Res 2023; 64:105-116. [PMID: 36271658 DOI: 10.1080/03008207.2022.2120392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
PURPOSE As the population ages, there is an increased risk of fracture and morbidity diseases associated with aging, such as age-related osteoporosis and other bone diseases linked to aging skeletons. RESULTS Several bone-related cells, including multipotent bone mesenchymal stem cells, osteoblasts that form bone tissue, and osteoclasts that break it down, are in symbiotic relationships throughout life. Growing evidence indicates that epigenetic modifications of cells caused by aging contribute to compromised bone remodeling and lead to osteoporosis. A number of epigenetic mechanisms are at play, including DNA/RNA modifications, histone modifications, microRNAs (miRNAs), and long noncoding RNAs (lncRNAs), as well as chromatin remodeling. CONCLUSION In this review, we summarized the epigenetic modifications of different bone-related cells during the development and progression of osteoporosis associated with aging. Additionally, we described a compensatory recovery mechanism under epigenetic regulation that may lead to new strategies for regulating bone remodeling in age-related osteoporosis.
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Affiliation(s)
- Wenyue Yu
- School and Hospital of Stomatology, Liaoning Provincial Key Laboratory of Oral Diseases, China Medical University, Shenyang, China
| | - He-Ling Wang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Jianying Zhang
- Xiangya School of Stomatology, Central South University, Changsha, China
| | - Chengcheng Yin
- School and Hospital of Stomatology, Liaoning Provincial Key Laboratory of Oral Diseases, China Medical University, Shenyang, China
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8
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Ramasamy D, Rao AKDM, Balaiah M, Vittal Rangan A, Sundersingh S, Veluswami S, Thangarajan R, Mani S. Locus-Specific Enrichment Analysis of 5-Hydroxymethylcytosine Reveals Novel Genes Associated with Breast Carcinogenesis. Cells 2022; 11:cells11192939. [PMID: 36230901 PMCID: PMC9562672 DOI: 10.3390/cells11192939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 12/03/2022] Open
Abstract
Highlights Abstract An imbalance in DNA methylation is a hallmark epigenetic alteration in cancer. The conversion of 5-methylcytosine (5-mC) to 5-hydroxymethyl cytosine (5-hmC), which causes the imbalance, results in aberrant gene expression. The precise functional role of 5-hydroxymethylcytosine in breast cancer remains elusive. In this study, we describe the landscape of 5-mC and 5-hmC and their association with breast cancer development. We found a distinguishable global loss of 5-hmC in the localized and invasive types of breast cancer that strongly correlate with TET expression. Genome-wide analysis revealed a unique 5-mC and 5-hmC signature in breast cancer. The differentially methylated regions (DMRs) were primarily concentrated in the proximal regulatory regions such as the promoters and UTRs, while the differentially hydroxymethylated regions (DhMRs) were densely packed in the distal regulatory regions, such as the intergenic regions (>−5 kb from TSSs). Our results indicate 4809 DMRs and 4841 DhMRs associated with breast cancer. Validation of nine 5-hmC enriched loci in a distinct set of breast cancer and normal samples positively correlated with their corresponding gene expression. The novel 5-hmC candidates such as TXNL1, and CNIH3 implicate a pro-oncogenic role in breast cancer. Overall, these results provide new insights into the loci-specific accumulation of 5-mC and 5-hmC, which are aberrantly methylated and demethylated in breast cancer.
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Affiliation(s)
- Deepa Ramasamy
- Department of Molecular Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai 600036, Tamilnadu, India
| | | | - Meenakumari Balaiah
- Department of Molecular Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai 600036, Tamilnadu, India
| | - Arvinden Vittal Rangan
- Department of Molecular Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai 600036, Tamilnadu, India
| | - Shirley Sundersingh
- Department of Oncopathology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai 600036, Tamilnadu, India
| | - Sridevi Veluswami
- Department of Surgical Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai 600036, Tamilnadu, India
| | - Rajkumar Thangarajan
- Department of Molecular Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai 600036, Tamilnadu, India
| | - Samson Mani
- Department of Molecular Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai 600036, Tamilnadu, India
- Correspondence: ; Tel.: +91-44-22350131 (ext. 196)
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9
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Ahmed YW, Alemu BA, Bekele SA, Gizaw ST, Zerihun MF, Wabalo EK, Teklemariam MD, Mihrete TK, Hanurry EY, Amogne TG, Gebrehiwot AD, Berga TN, Haile EA, Edo DO, Alemu BD. Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing. Clin Epigenetics 2022; 14:107. [PMID: 36030244 PMCID: PMC9419648 DOI: 10.1186/s13148-022-01323-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.
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Affiliation(s)
- Yohannis Wondwosen Ahmed
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia.
| | - Berhan Ababaw Alemu
- Department of Medical Biochemistry, School of Medicine, St. Paul's Hospital, Millennium Medical College, Addis Ababa, Ethiopia
| | - Sisay Addisu Bekele
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Solomon Tebeje Gizaw
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Muluken Fekadie Zerihun
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endriyas Kelta Wabalo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Maria Degef Teklemariam
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tsehayneh Kelemu Mihrete
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endris Yibru Hanurry
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tensae Gebru Amogne
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Assaye Desalegne Gebrehiwot
- Department of Medical Anatomy, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tamirat Nida Berga
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Ebsitu Abate Haile
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Dessiet Oma Edo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Bizuwork Derebew Alemu
- Department of Statistics, College of Natural and Computational Sciences, Mizan Tepi University, Tepi, Ethiopia
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10
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Govender P, Ghai M, Okpeku M. Sex-specific DNA methylation: impact on human health and development. Mol Genet Genomics 2022; 297:1451-1466. [PMID: 35969270 DOI: 10.1007/s00438-022-01935-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/28/2022] [Indexed: 11/26/2022]
Abstract
Human evolution has shaped gender differences between males and females. Over the years, scientific studies have proposed that epigenetic modifications significantly influence sex-specific differences. The evolution of sex chromosomes with epigenetics as the driving force may have led to one sex being more adaptable than the other when exposed to various factors over time. Identifying and understanding sex-specific differences, particularly in DNA methylation, will help determine how each gender responds to factors, such as disease susceptibility, environmental exposure, brain development and neurodegeneration. From a medicine and health standpoint, sex-specific methylation studies have shed light on human disease severity, progression, and response to therapeutic intervention. Interesting findings in gender incongruent individuals highlight the role of genetic makeup in influencing DNA methylation differences. Sex-specific DNA methylation studies will empower the biotechnology and pharmaceutical industry with more knowledge to identify biomarkers, design and develop sex bias drugs leading to better treatment in men and women based on their response to different diseases.
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Affiliation(s)
- Priyanka Govender
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Meenu Ghai
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa.
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
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11
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Varma SJ, Calvani E, Grüning NM, Messner CB, Grayson N, Capuano F, Mülleder M, Ralser M. Global analysis of cytosine and adenine DNA modifications across the tree of life. eLife 2022; 11:81002. [PMID: 35900202 PMCID: PMC9333990 DOI: 10.7554/elife.81002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 12/12/2022] Open
Abstract
Interpreting the function and metabolism of enzymatic DNA modifications requires both position-specific and global quantities. Sequencing-based techniques that deliver the former have become broadly accessible, but analytical methods for the global quantification of DNA modifications have thus far been applied mostly to individual problems. We established a mass spectrometric method for the sensitive and accurate quantification of multiple enzymatic DNA modifications. Then, we isolated DNA from 124 archean, bacterial, fungal, plant, and mammalian species, and several tissues and created a resource of global DNA modification quantities. Our dataset provides insights into the general nature of enzymatic DNA modifications, reveals unique biological cases, and provides complementary quantitative information to normalize and assess the accuracy of sequencing-based detection of DNA modifications. We report that only three of the studied DNA modifications, methylcytosine (5mdC), methyladenine (N6mdA) and hydroxymethylcytosine (5hmdC), were detected above a picomolar detection limit across species, and dominated in higher eukaryotes (5mdC), in bacteria (N6mdA), or the vertebrate central nervous systems (5hmdC). All three modifications were detected simultaneously in only one of the tested species, Raphanus sativus. In contrast, these modifications were either absent or detected only at trace quantities, across all yeasts and insect genomes studied. Further, we reveal interesting biological cases. For instance, in Allium cepa, Helianthus annuus, or Andropogon gerardi, more than 35% of cytosines were methylated. Additionally, next to the mammlian CNS, 5hmdC was also detected in plants like Lepidium sativum and was found on 8% of cytosines in the Garra barreimiae brain samples. Thus, identifying unexpected levels of DNA modifications in several wild species, our resource underscores the need to address biological diversity for studying DNA modifications.
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Affiliation(s)
| | - Enrica Calvani
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom.,Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
| | - Nana-Maria Grüning
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Christoph B Messner
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom.,Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas Grayson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Floriana Capuano
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
| | - Michael Mülleder
- Core Facility-High Throughput Mass Spectrometry, Charité Universitätsmedizin, Berlin, Germany
| | - Markus Ralser
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany.,The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom.,Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
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12
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Zhang Z, He T, Qi Y, Dai Y, Lao K, Gou X. Rapid and highly specific detection of site-specific 5-hydroxymethylcytosine based on peroxotungstate oxidation and mismatch ligation-based LAMP. RSC Adv 2022; 12:19885-19889. [PMID: 35865199 PMCID: PMC9261916 DOI: 10.1039/d2ra03310k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/21/2022] [Indexed: 11/21/2022] Open
Abstract
We have developed a rapid and specific method for site-specific 5-hydroxymethylcytosine (5hmC) quantification at single-base resolution. This bisulfite-free method integrates the peroxotungstate oxidization with the mismatched probe-assisted ligation to guarantee the specificity. Moreover, the high-efficiency LAMP also makes the proposed method suitable for the detection of low-content samples. A facile and highly specific mismatch ligation-based amplification platform for quantification of site-specific 5hmC at single base resolution in low-content samples.![]()
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Affiliation(s)
- Zhenhao Zhang
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603.,School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710062 Shaanxi Province P. R. China
| | - Tong He
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603.,School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710062 Shaanxi Province P. R. China
| | - Yan Qi
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603
| | - Yuxuan Dai
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603
| | - Kejing Lao
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603
| | - Xingchun Gou
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603
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13
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Qiu T, Wang X, Du F, Hu X, Sun F, Song C, Zhao J. TET1 mutations as a predictive biomarker for immune checkpoint inhibitors in colon adenocarcinoma. World J Surg Oncol 2022; 20:115. [PMID: 35395805 PMCID: PMC8991851 DOI: 10.1186/s12957-022-02581-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/19/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The ten-eleven translocation 1 (TET1), which is essential for active DNA demethylation, plays a multifaceted role in the pathogenesis of colorectal cancer. The study has demonstrated the association of TET1 mutations with a high response to immune checkpoint inhibitors (ICIs) in diverse cancers. However, the relationship between TET1 mutations and the response to ICIs in colon cancer is still lacking. METHODS The prognosis, predictive markers, immune characteristics, mutation number of DNA damage repair (DDR) pathways, pathway enrichment, and drug sensitivity conditions were all compared between TET1-mutated and wild-type patients with colon adenocarcinoma (COAD). RESULTS The overall survival of patients with TET1 mutations in the ICI-treated cohort was significantly longer than those without (p = 0.0059). Compared with the wild-type patients, TET1-mutated patients had higher tumor mutational burden and neoantigen load, enhanced abundance of tumor-infiltrating immune cells, increased expression of immune-related genes, and mutation number of DDR pathways. Additionally, the patients with TET1 mutations were found to be more sensitive to lapatinib and 5-fluorouracil. CONCLUSION These findings suggest that TET1 mutations may serve as a potential biomarker for the response to ICIs in COAD patients.
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Affiliation(s)
- Tianzhu Qiu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Xiaoxuan Wang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, 210042, Jiangsu, China
| | - Furong Du
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, 210042, Jiangsu, China
| | - Xiangjing Hu
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, 210042, Jiangsu, China
| | - Fujun Sun
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, 210042, Jiangsu, China
| | - Chao Song
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, 210042, Jiangsu, China. .,Henan Key Laboratory of Precision Medicine, Zhengzhou, 450052, Henan, China.
| | - Jie Zhao
- Henan Key Laboratory of Precision Medicine, Zhengzhou, 450052, Henan, China. .,National Engineering Laboratory for Internet Medical Systems and Applications, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
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14
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Chen MY, Gui Z, Chen KK, Ding JH, He JG, Xiong J, Li JL, Wang J, Yuan BF, Feng YQ. Adolescent alcohol exposure alters DNA and RNA modifications in peripheral blood by liquid chromatography-tandem mass spectrometry analysis. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.08.094] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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15
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Lejart A, Zentout S, Chapuis C, D'Augustin O, Smith R, Salbert G, Huet S. The N-terminal domain of TET1 promotes the formation of dense chromatin regions refractory to transcription. Chromosoma 2022; 131:47-58. [PMID: 35235010 DOI: 10.1007/s00412-022-00769-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 11/03/2022]
Abstract
TET (ten-eleven translocation) enzymes initiate active cytosine demethylation via the oxidation of 5-methylcytosine. TET1 is composed of a C-terminal domain, which bears the catalytic activity of the enzyme, and a N-terminal region that is less well characterized except for the CXXC domain responsible for the targeting to CpG islands. While cytosine demethylation induced by TET1 promotes transcription, this protein also interacts with chromatin-regulating factors that rather silence this process, the coordination between these two opposite functions of TET1 being unclear. In the present work, we uncover a new function of the N-terminal part of the TET1 protein in the regulation of the chromatin architecture. This domain of the protein promotes the establishment of a compact chromatin architecture displaying reduced exchange rate of core histones and partial dissociation of the histone linker. This chromatin reorganization process, which does not rely on the CXXC domain, is associated with a global shutdown of transcription and an increase in heterochromatin-associated histone epigenetic marks. Based on these findings, we propose that the dense chromatin organization generated by the N-terminal domain of TET1 could contribute to restraining the transcription enhancement induced by the DNA demethylation activity of this enzyme.
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Affiliation(s)
- Audrey Lejart
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
| | - Siham Zentout
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
| | - Catherine Chapuis
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
| | - Ostiane D'Augustin
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
- Institut de Biologie François Jacob, Institute of Cellular and Molecular Radiobiology, Université Paris-Saclay, Université de Paris, CEA, 92265, Fontenay-aux-Roses, France
| | - Rebecca Smith
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
| | - Gilles Salbert
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France.
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France.
- Institut Universitaire de France, Paris, France.
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16
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An Improved Approach for Practical Synthesis of 5-Hydroxymethyl-2′-deoxycytidine (5hmdC) Phosphoramidite and Triphosphate. Molecules 2022; 27:molecules27030749. [PMID: 35164012 PMCID: PMC8839764 DOI: 10.3390/molecules27030749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/16/2022] Open
Abstract
5-Hydroxymethyl-2′-deoxycytidine (5hmdC) phosphoramidite and triphosphate are important building blocks in 5hmdC-containing DNA synthesis for epigenetic studies. However, efficient and practical methods for the synthesis of these compounds are still limited. The current research provides an intensively improved synthetic method that enables the preparation of commercially available cyanoethyl-protected 5hmdC phosphoramidite with an overall yield of 39% on 5 g scale. On the basis of facile and efficient accesses to cyanoethyl protected-5hmdU and 5hmdC intermediates, two efficient synthetic routes for 5hmdC triphosphate were also developed.
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17
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Xie NB, Wang M, Ji TT, Guo X, Ding JH, Yuan BF, Feng YQ. Bisulfite-free and single-nucleotide resolution sequencing of DNA epigenetic modification of 5-hydroxymethylcytosine by engineered deaminase. Chem Sci 2022; 13:7046-7056. [PMID: 35774177 PMCID: PMC9200132 DOI: 10.1039/d2sc01052f] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/23/2022] [Indexed: 11/21/2022] Open
Abstract
The discovery of 5-hydroxymethylcytosine (5hmC) in mammalian genomes is a landmark in epigenomics study. Similar to 5-methylcytosine (5mC), 5hmC is viewed a critical epigenetic modification. Deciphering the functions of 5hmC...
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Affiliation(s)
- Neng-Bin Xie
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China
- School of Public Health, Wuhan University Wuhan 430071 China
| | - Min Wang
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China
| | - Tong-Tong Ji
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China
| | - Xia Guo
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China
| | - Jiang-Hui Ding
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China
| | - Bi-Feng Yuan
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China
- School of Public Health, Wuhan University Wuhan 430071 China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University Wuhan 430071 China
| | - Yu-Qi Feng
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China
- School of Public Health, Wuhan University Wuhan 430071 China
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18
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Gracias F, Ruiz-Larrabeiti O, Vaňková Hausnerová V, Pohl R, Klepetářová B, Sýkorová V, Krásný L, Hocek M. Homologues of epigenetic pyrimidines: 5-alkyl-, 5-hydroxyalkyl and 5-acyluracil and -cytosine nucleotides: synthesis, enzymatic incorporation into DNA and effect on transcription with bacterial RNA polymerase. RSC Chem Biol 2022; 3:1069-1075. [PMID: 35975001 PMCID: PMC9347353 DOI: 10.1039/d2cb00133k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/23/2022] [Indexed: 12/17/2022] Open
Abstract
Homologues of natural epigenetic pyrimidine nucleosides and nucleotides were designed and synthesized. They included 5-ethyl-, 5-propyl-, 5-(1-hydroxyethyl)-, 5-(1-hydroxypropyl)- and 5-acetyl- and 5-propionylcytosine and -uracil 2′-deoxyribonucleosides and their corresponding 5′-O-triphosphates (dNXTPs). The epimers of 5-(1-hydroxyethyl)- and 5-(1-hydroxypropyl)pyrimidine nucleosides were separated and their absolute configuration was determined by a combination of X-ray and NMR analysis. The modified dNXTPs were used as substrates for PCR synthesis of modified DNA templates used for the study of transcription with bacterial RNA polymerase. Fundamental differences in transcription efficiency were observed, depending on the various modifications. The most notable effects included pronounced stimulation of transcription from 5-ethyluracil-bearing templates (200% transcription yield compared to natural thymine) and an enhancing effect of 5-acetylcytosine versus inhibiting effect of 5-acetyluracil. In summary, these results reveal that RNA polymerase copes with dramatically altered DNA structure and suggest that these nucleobases could potentially play roles as artificial epigenetic DNA nucleobases. Nucleotides derived from homologues of epigenetic pyrimidine bases were prepared and used for polymerase synthesis of modified DNA templates. Interesting effects of the substituents on PCR and transcription have been observed.![]()
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Affiliation(s)
- Filip Gracias
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
| | - Olatz Ruiz-Larrabeiti
- Lab. of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague 4, Czech Republic
| | - Viola Vaňková Hausnerová
- Lab. of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague 4, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
| | - Blanka Klepetářová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
| | - Libor Krásný
- Lab. of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220, Prague 4, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague 2, Czech Republic
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19
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Ding J, Zhou Y, Wang Q, Ai S. Photoelectrochemical biosensor for DNA hydroxymethylation detection based on the enhanced photoactivity of in-situ synthesized Bi 4NbO 8Cl@Bi 2S 3 heterojunction. Biosens Bioelectron 2021; 194:113580. [PMID: 34454344 DOI: 10.1016/j.bios.2021.113580] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/09/2021] [Accepted: 08/20/2021] [Indexed: 12/14/2022]
Abstract
As an important epigenetic modification, 5-hydroxymethylcytosine (5hmC) aroused wide concern about the distribution and the function. Due to the necessity of 5hmC detection, a novel photoelectrochemical (PEC) biosensor was established based on the in-situ generated heterojunction of Bi4NbO8Cl@Bi2S3, which was employed as the substrate material with excellent photoelectric property. The specific recognition of 5hmC relied on the covalent reaction between -CH2OH of 5hmC and -SH on the substrate electrode under the catalysis of M.HhaI methyltransferase. Afterwards, ZrO2 was used as signal amplification unit capturing by the specific reaction of Zr with the phosphate group of 5hmC. The experimental results demonstrated well specificity and sensitivity of this biosensor. Under optimal conditions, the linear relationship between the photocurrent and the logarithm value of 5hmC concentration was constructed with the range from 0.3 to 300 nM and the detection limit of 0.0779 nM (S/N = 3). The procedures of constructing this biosensor were compact and convenient, and this biosensor realized actual detection of 5hmC level in wheat sample. Significantly, this biosensor was applied to a preliminary study that the heavy metal Pb2+ and the perfluorooctanoic acid influence the expression of 5hmC in the genomic DNA of wheat seedling roots and leaves.
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Affiliation(s)
- Jia Ding
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, PR China
| | - Yunlei Zhou
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, PR China.
| | - Qian Wang
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, PR China
| | - Shiyun Ai
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, PR China
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20
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Sinha SK, Roy TK, Modak A, Maiti D. Enabling the Facile Synthesis of Arenes by Transition Metal Catalyzed Decarbonylation Methodology. CHEM REC 2021; 21:3990-3999. [PMID: 34713555 DOI: 10.1002/tcr.202100244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 11/11/2022]
Abstract
Transition metal-catalyzed decarbonylation is an essential paradigm of synthetic organic chemistry. Decarbonylation offers a unique pathway to decoding the skeletal structure of arenes and enabling easy synthesis of structurally complicated molecules. Due to the omnipresence of carbonyl groups in a wide array of synthetically important complex molecules, the variety and scope of these transformations are enormous. As a result, the development of transition metal catalysts in such a simple decarbonylation reaction ranks among one of the most important topics in synthetic organic chemistry. Transition metals that have been employed range from 3d metals like V to second-row transition metals like Pd. The growing potential of this methodology has driven the pioneers of synthetic organic chemistry into delving into the details of this transition metal-catalyzed decarbonylation pathways. This review aims to take the readers through the employment of transition metals in various decarbonylation processes developed by our group, sticking not only to the scope and diversification of synthetically complex molecules, but also enabling the readers to understand the mechanistic insights, through computational and kinetic studies put forward in such reaction protocol, hoping to pave the way for future organic chemists to delve and hopefully solve the unique problems associated with this protocol.
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Affiliation(s)
- Soumya Kumar Sinha
- Department of Chemistry, Indian Institute of Technology Bombay Powai, Mumbai, 400076, India
| | - Triptesh Kumar Roy
- Department of Chemistry, Indian Institute of Technology Bombay Powai, Mumbai, 400076, India
| | - Atanu Modak
- Department of Chemistry, Indian Institute of Technology Bombay Powai, Mumbai, 400076, India
| | - Debabrata Maiti
- Department of Chemistry, Indian Institute of Technology Bombay Powai, Mumbai, 400076, India
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21
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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22
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Gabius HJ, Cudic M, Diercks T, Kaltner H, Kopitz J, Mayo KH, Murphy PV, Oscarson S, Roy R, Schedlbauer A, Toegel S, Romero A. What is the Sugar Code? Chembiochem 2021; 23:e202100327. [PMID: 34496130 PMCID: PMC8901795 DOI: 10.1002/cbic.202100327] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/07/2021] [Indexed: 12/18/2022]
Abstract
A code is defined by the nature of the symbols, which are used to generate information‐storing combinations (e. g. oligo‐ and polymers). Like nucleic acids and proteins, oligo‐ and polysaccharides are ubiquitous, and they are a biochemical platform for establishing molecular messages. Of note, the letters of the sugar code system (third alphabet of life) excel in coding capacity by making an unsurpassed versatility for isomer (code word) formation possible by variability in anomery and linkage position of the glycosidic bond, ring size and branching. The enzymatic machinery for glycan biosynthesis (writers) realizes this enormous potential for building a large vocabulary. It includes possibilities for dynamic editing/erasing as known from nucleic acids and proteins. Matching the glycome diversity, a large panel of sugar receptors (lectins) has developed based on more than a dozen folds. Lectins ‘read’ the glycan‐encoded information. Hydrogen/coordination bonding and ionic pairing together with stacking and C−H/π‐interactions as well as modes of spatial glycan presentation underlie the selectivity and specificity of glycan‐lectin recognition. Modular design of lectins together with glycan display and the nature of the cognate glycoconjugate account for the large number of post‐binding events. They give an entry to the glycan vocabulary its functional, often context‐dependent meaning(s), hereby building the dictionary of the sugar code.
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Affiliation(s)
- Hans-Joachim Gabius
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539, Munich, Germany
| | - Maré Cudic
- Department of Chemistry and Biochemistry, Charles E. Schmidt College of Science, Florida Atlantic University, 777 Glades Road, Boca Raton, Florida, 33431, USA
| | - Tammo Diercks
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160, Derio, Bizkaia, Spain
| | - Herbert Kaltner
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539, Munich, Germany
| | - Jürgen Kopitz
- Institute of Pathology, Department of Applied Tumor Biology, Faculty of Medicine, Ruprecht-Karls-University Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Kevin H Mayo
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Paul V Murphy
- CÚRAM - SFI Research Centre for Medical Devices and the, School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - René Roy
- Département de Chimie et Biochimie, Université du Québec à Montréal, Case Postale 888, Succ. Centre-Ville Montréal, Québec, H3C 3P8, Canada
| | - Andreas Schedlbauer
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160, Derio, Bizkaia, Spain
| | - Stefan Toegel
- Karl Chiari Lab for Orthopaedic Biology, Department of Orthopedics and Trauma Surgery, Medical University of Vienna, Vienna, Austria
| | - Antonio Romero
- Department of Structural and Chemical Biology, CIB Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
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23
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Korytiaková E, Kamińska E, Müller M, Carell T. Deformylation of 5-Formylcytidine in Different Cell Types. Angew Chem Int Ed Engl 2021; 60:16869-16873. [PMID: 34110681 PMCID: PMC8362038 DOI: 10.1002/anie.202107089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Indexed: 12/19/2022]
Abstract
Epigenetic programming of cells requires methylation of deoxycytidines (dC) to 5-methyl-dC (mdC) followed by oxidation to 5-hydroxymethyl-dC (hmdC), 5-formyl-dC (fdC), and 5-carboxy-dC (cadC). Subsequent transformation of fdC and cadC back to dC by various pathways establishes a chemical intra-genetic control circle. One of the discussed pathways involves the Tdg-independent deformylation of fdC directly to dC. Here we report the synthesis of a fluorinated fdC feeding probe (F-fdC) to study direct deformylation to F-dC. The synthesis was performed along a novel pathway that circumvents any F-dC as a reaction intermediate to avoid contamination interference. Feeding of F-fdC and observation of F-dC formation in vivo allowed us to gain insights into the Tdg-independent removal process. While deformylation was shown to occur in stem cells, we here provide data that prove deformylation also in different somatic cell types. We also investigated active demethylation in a non-dividing neurogenin-inducible system of iPS cells that differentiate into bipolar neurons.
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Affiliation(s)
- Eva Korytiaková
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Ewelina Kamińska
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Markus Müller
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Thomas Carell
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
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24
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Han Y, Ji L, Guan Y, Ma M, Li P, Xue Y, Zhang Y, Huang W, Gong Y, Jiang L, Wang X, Xie H, Zhou B, Wang J, Wang J, Han J, Deng Y, Yi X, Gao F, Huang J. An epigenomic landscape of cervical intraepithelial neoplasia and cervical cancer using single-base resolution methylome and hydroxymethylome. Clin Transl Med 2021; 11:e498. [PMID: 34323415 PMCID: PMC8288011 DOI: 10.1002/ctm2.498] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 06/22/2021] [Accepted: 06/27/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Cervical cancer (CC) is the second leading cause of cancer death among women worldwide. Epigenetic regulation of gene expression through DNA methylation and hydroxymethylation plays a pivotal role during tumorigenesis. In this study, to analyze the epigenomic landscape and identify potential biomarkers for CCs, we selected a series of samples from normal to cervical intra-epithelial neoplasia (CINs) to CCs and performed an integrative analysis of whole-genome bisulfite sequencing (WGBS-seq), oxidative WGBS, RNA-seq, and external histone modifications profiling data. RESULTS In the development and progression of CC, there were genome-wide hypo-methylation and hypo-hydroxymethylation, accompanied by local hyper-methylation and hyper-hydroxymethylation. Hydroxymethylation prefers to distribute in the CpG islands and CpG shores, as displayed a trend of gradual decline from health to CIN2, while a trend of increase from CIN3 to CC. The differentially methylated and hydroxymethylated region-associated genes both enriched in Hippo and other cancer-related signaling pathways that drive cervical carcinogenesis. Furthermore, we identified eight novel differentially methylated/hydroxymethylated-associated genes (DES, MAL, MTIF2, PIP5K1A, RPS6KA6, ANGEL2, MPP, and PAPSS2) significantly correlated with the overall survival of CC. In addition, no any correlation was observed between methylation or hydroxymethylation levels and somatic copy number variations in CINs and CCs. CONCLUSION Our current study systematically delineates the map of methylome and hydroxymethylome from CINs to CC, and some differentially methylated/hydroxymethylated-associated genes can be used as the potential epigenetic biomarkers in CC prognosis.
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Affiliation(s)
- Yingxin Han
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Centre for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | | | - Yanfang Guan
- Department of Computer Science and TechnologySchool of Electronic and Information EngineeringXi'an Jiao Tong UniversityXi'anChina
- GenePlus‐BeijingBeijingChina
| | | | | | - Yinge Xue
- Shanghai FLY Medical LaboratoryShanghaiChina
| | | | - Wanqiu Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Centre for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | | | - Li Jiang
- The Department of Obstetrics and GynecologyXinhua Hospital affiliated to Shanghai Jiao Tong UniversityShanghaiChina
| | - Xipeng Wang
- The Department of Obstetrics and GynecologyXinhua Hospital affiliated to Shanghai Jiao Tong UniversityShanghaiChina
| | - Hong Xie
- The Department of Obstetrics and GynecologyShenzhen People's HospitalShenzhenChina
| | - Boping Zhou
- The Department of Obstetrics and GynecologyShenzhen People's HospitalShenzhenChina
| | - Jiayin Wang
- Department of Computer Science and TechnologySchool of Electronic and Information EngineeringXi'an Jiao Tong UniversityXi'anChina
| | - Junwen Wang
- Genome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Jinghua Han
- Genome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Yuliang Deng
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Centre for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Xin Yi
- GenePlus‐BeijingBeijingChina
| | - Fei Gao
- Genome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
- Comparative Pediatrics and NutritionDepartment of Veterinary and Animal SciencesFaculty of Health and Medical SciencesUniversity of CopenhagenFrederiksbergDenmark
| | - Jian Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Centre for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
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25
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Korytiaková E, Kamińska E, Müller M, Carell T. Deformylierung von 5‐Formylcytidin in unterschiedlichen Zelltypen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Eva Korytiaková
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Ewelina Kamińska
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Markus Müller
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Thomas Carell
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
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26
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Zhu BZ, Tang M, Huang CH, Mao L, Shao J. Mechanistic Study on Oxidative DNA Damage and Modifications by Haloquinoid Carcinogenic Intermediates and Disinfection Byproducts. Chem Res Toxicol 2021; 34:1701-1712. [PMID: 34143619 DOI: 10.1021/acs.chemrestox.1c00158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Haloquinones (XQs) are a group of carcinogenic intermediates of the haloaromatic environmental pollutants and newly identified chlorination disinfection byproducts (DBPs) in drinking water. The highly reactive hydroxyl radicals/alkoxyl radicals and quinone enoxy/ketoxy radicals were found to arise in XQs and H2O2 or organic hydroperoxides system, independent of transition-metal ions. However, it was not clear whether these haloquinoid carcinogens and hydroperoxides can cause oxidative DNA damage and modifications, and if so, what are the underlying molecular mechanisms. We found that 8-oxodeoxyguanosine (8-oxodG), DNA strand breaks, and three methyl oxidation products could arise when DNA was treated with tetrachloro-1,4-benzoquinone and H2O2 via a metal-independent and intercalation-enhanced oxidation mechanism. Similar effects were observed with other XQs, which are generally more efficient than the typical Fenton system. We further extended our studies from isolated DNA to genomic DNA in living cells. We also found that potent oxidation of DNA to the more mutagenic imidazolone dIz could be induced by XQs and organic hydroperoxides such as t-butylhydroperoxide or the physiologically relevant hydroperoxide 13S-hydroperoxy-9Z,11E-octadecadienoic acid via an unprecedented quinone-enoxy radical-mediated mechanism. These findings should provide new perspectives to explain the potential genotoxicity, mutagenesis, and carcinogenicity for the ubiquitous haloquinoid carcinogenic intermediates and DBPs.
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Affiliation(s)
- Ben-Zhan Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Miao Tang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Chun-Hua Huang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Li Mao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Jie Shao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
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27
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Schelter F, Kirchner A, Traube FR, Müller M, Steglich W, Carell T. 5-Hydroxymethyl-, 5-Formyl- and 5-Carboxydeoxycytidines as Oxidative Lesions and Epigenetic Marks. Chemistry 2021; 27:8100-8104. [PMID: 33769637 PMCID: PMC8252671 DOI: 10.1002/chem.202100551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Indexed: 01/20/2023]
Abstract
The four non-canonical nucleotides in the human genome 5-methyl-, 5-hydroxymethyl-, 5-formyl- and 5-carboxydeoxycytidine (mdC, hmdC, fdC and cadC) form a second layer of epigenetic information that contributes to the regulation of gene expression. Formation of the oxidized nucleotides hmdC, fdC and cadC requires oxidation of mdC by ten-eleven translocation (Tet) enzymes that require oxygen, Fe(II) and α-ketoglutarate as cosubstrates. Although these oxidized forms of mdC are widespread in mammalian genomes, experimental evidence for their presence in fungi and plants is ambiguous. This vagueness is caused by the fact that these oxidized mdC derivatives are also formed as oxidative lesions, resulting in unclear basal levels that are likely to have no epigenetic function. Here, we report the xdC levels in the fungus Amanita muscaria in comparison to murine embryonic stem cells (mESCs), HEK cells and induced pluripotent stem cells (iPSCs), to obtain information about the basal levels of hmdC, fdC and cadC as DNA lesions in the genome.
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Affiliation(s)
- Florian Schelter
- Ludwigs-Maximilian-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Angie Kirchner
- Ludwigs-Maximilian-Universität MünchenButenandtstr. 5–1381377MunichGermany
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeCB2 0REUK
| | | | - Markus Müller
- Ludwigs-Maximilian-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Wolfgang Steglich
- Ludwigs-Maximilian-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Thomas Carell
- Ludwigs-Maximilian-Universität MünchenButenandtstr. 5–1381377MunichGermany
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28
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Wei X, Yu L, Zhang Y, Li X, Wu H, Jiang J, Qing Y, Miao Z, Fang Q. The Role of Tet2-mediated Hydroxymethylation in Poststroke Depression. Neuroscience 2021; 461:118-129. [PMID: 33689862 DOI: 10.1016/j.neuroscience.2021.02.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/25/2021] [Accepted: 02/27/2021] [Indexed: 12/12/2022]
Abstract
Poststroke depression (PSD) is a common complication of stroke and has long been a serious threat to human health. PSD greatly affects neurological recovery, quality of life and mortality. Recent studies have shown that 5-hydroxymethylcytosine (5hmC), an important epigenetic modification, is enriched in the brain and associated with many neurological diseases. However, its role in PSD is still unclear. In this study, middle cerebral artery occlusion (MCAO) and spatial restraint stress were used to successfully induce a PSD mouse model and resulted in reduced 5hmC levels, which were caused by Tet2. Furthermore, genome-wide analysis of 5hmC revealed that differentially hydroxymethylated regions (DhMRs) were associated with PSD. DhMRs were enriched among genes involved in the Wnt signaling pathway, neuron development and learning or memory. In particular,DhMRs were strongly enriched in genes with lymphoid enhancer factor 1 (LEF1) binding motifs. Finally, we demonstrated that decreases in TET2 expression in the brain caused PSD by decreasing Wnt/β-catenin/LEF1 pathway signaling to promote inflammatory factor IL-18 expression. In conclusion, our data highlight the potential for 5hmC modification as a therapeutic target for PSD.
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Affiliation(s)
- Xin Wei
- Department of Neurology, the First Affiliated Hospital of Soochow University, Suzhou City, China
| | - Liqiang Yu
- Department of Neurology, the First Affiliated Hospital of Soochow University, Suzhou City, China
| | - Yujuan Zhang
- Experiment Center, Medicine College of Soochow University, Suzhou City, China
| | - Xiaojing Li
- Department of Neurology, Suzhou Hospital Affiliated to Nanjing Medical University, Suzhou, Jiangsu, China; Department of Neurology, Suzhou Science and Technology Town Hospital, Suzhou, Jiangsu, China
| | - Hainan Wu
- College of Forestry, Nanjing Forestry University, Nanjing City, Jiangsu, China
| | - Jianhua Jiang
- Department of Neurology, the First Affiliated Hospital of Soochow University, Suzhou City, China
| | - Yiren Qing
- Department of Neurology, the First Affiliated Hospital of Soochow University, Suzhou City, China
| | - Zhigang Miao
- Institute of Neuroscience, Soochow University, Suzhou City, China; Jiangsu Key Laboratory of Neuropsychiatric Diseases, Soochow University, Suzhou, Jiangsu 215123, China.
| | - Qi Fang
- Department of Neurology, the First Affiliated Hospital of Soochow University, Suzhou City, China.
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29
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Sharapova T, Talaty N, Buck WR, Fossey S, Liguori MJ, Van Vleet TR. Reduced hepatic global hydroxymethylation in mice treated with non-genotoxic carcinogens is transiently reversible with a methyl supplemented diet. Toxicol Appl Pharmacol 2021; 415:115439. [PMID: 33549593 DOI: 10.1016/j.taap.2021.115439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/20/2021] [Accepted: 01/31/2021] [Indexed: 01/05/2023]
Abstract
Non-genotoxic carcinogens (NGCs) are known to cause perturbations in DNA methylation, which can be an early event leading to changes in gene expression and the onset of carcinogenicity. Phenobarbital (PB) has been shown to alter liver DNA methylation and hydroxymethylation patterns in mice in a time dependent manner. The goals of this study were to assess if clofibrate (CFB), a well-studied rodent NGC, would produce epigenetic changes in mice similar to PB, and if a methyl donor supplementation (MDS) would modulate epigenetic and gene expression changes induced by phenobarbital. CByB6F1 mice were treated with 0.5% clofibrate or 0.14% phenobarbital for 7 and 28 days. A subgroup of PB treated and control mice were also fed MDS diet. Liquid Chromatography-Ionization Mass Spectrometry (LC-MS) was used to quantify global liver 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) levels. Gene expression analysis was conducted using Affymetrix microarrays. A decrease in liver 5hmC but not 5mC levels was observed upon treatment with both CFB and PB with varying time of onset. We observed moderate increases in 5hmC levels in PB-treated mice when exposed to MDS diet and lower expression levels of several phenobarbital induced genes involved in cell proliferation, growth, and invasion, suggesting an early modulating effect of methyl donor supplementation. Overall, epigenetic profiling can aid in identifying early mechanism-based biomarkers of non-genotoxic carcinogenicity and increases the quality of cancer risk assessment for candidate drugs. Global DNA methylation assessment by LC-MS is an informative first step toward understanding the risk of carcinogenicity.
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Affiliation(s)
- T Sharapova
- Investigative Toxicology and Pathology, AbbVie Inc., North Chicago, IL, United States.
| | - N Talaty
- Discovery Platform Technologies, AbbVie Inc., North Chicago, IL, United States
| | - W R Buck
- Investigative Toxicology and Pathology, AbbVie Inc., North Chicago, IL, United States
| | - S Fossey
- Investigative Toxicology and Pathology, AbbVie Inc., North Chicago, IL, United States
| | - M J Liguori
- Investigative Toxicology and Pathology, AbbVie Inc., North Chicago, IL, United States
| | - T R Van Vleet
- Investigative Toxicology and Pathology, AbbVie Inc., North Chicago, IL, United States
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30
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Li CC, Chen HY, Dong YH, Luo X, Hu J, Zhang CY. Advances in Detection of Epigenetic Modification—5-Hydroxymethylcytosine. ACTA CHIMICA SINICA 2021. [DOI: 10.6023/a20120564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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31
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Liu M, Li CC, Luo X, Ma F, Zhang CY. 5-Hydroxymethylcytosine Glucosylation-Triggered Helicase-Dependent Amplification-Based Fluorescent Biosensor for Sensitive Detection of β-Glucosyltransferase with Zero Background Signal. Anal Chem 2020; 92:16307-16313. [DOI: 10.1021/acs.analchem.0c04382] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Meng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Chen-chen Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; and College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Xiliang Luo
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; and College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Fei Ma
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Chun-yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
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32
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Ding J, Jiang W, Zhou Y, Yin H, Ai S. Electrochemiluminescence immunosensor for 5-hydroxymethylcytosine detection based on PAMAM-nanosilver‑nitrogen doped graphene nanocomposite. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114646] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Li S, Tollefsbol TO. DNA methylation methods: Global DNA methylation and methylomic analyses. Methods 2020; 187:28-43. [PMID: 33039572 DOI: 10.1016/j.ymeth.2020.10.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has significant involvement for numerous biological processes in health and disease. The function of methylation of cytosine bases in DNA was originally proposed as a "silencing" epigenetic marker and focused on promoter regions of genes for decades. Improved technologies and accumulating studies have been extending our understanding of the roles of DNA methylation to various genomic contexts including gene bodies, repeat sequences and transcriptional start sites. The demand for comprehensively describing DNA methylation patterns spawns a diversity of DNA methylation profiling technologies that target its genomic distribution. These approaches have enabled the measurement of cytosine methylation from specific loci at restricted regions to single-base-pair resolution on a genome-scale level. In this review, we discuss the different DNA methylation analysis technologies primarily based on the initial treatments of DNA samples: bisulfite conversion, endonuclease digestion and affinity enrichment, involving methodology evolution, principles, applications, and their relative merits. This review may offer referable information for the selection of various platforms for genome-wide analysis of DNA methylation.
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Affiliation(s)
- Shizhao Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States; Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, United States.
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34
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Zheng S, Tran A, Curry AM, White DS, Cen Y. Convenient synthesis of pyrimidine 2'-deoxyribonucleoside monophosphates with important epigenetic marks at the 5-position. Org Biomol Chem 2020; 18:5164-5173. [PMID: 32584362 DOI: 10.1039/d0ob00884b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Methyl groups of thymine and 5-methylcytosine (5mC) bases in DNA undergo endogenous oxidation damage. Additionally, 5mC residues can be enzymatically deaminated or oxidized through either genetic alterations or the newly identified epigenetic reprogramming pathway. Several methods have been developed to measure the formation of modified DNA nucleobases including 32P-postlabeling. However, the postlabeling method is often limited by the absence of authentic chemical standards. The synthesis of monophosphate standards of nucleotide oxidation products is complicated by the presence of additional functional groups on the modified bases that require complex protection and deprotection strategies. Due to the emerging interest in the pyrimidine oxidation products, the corresponding protected 3'-phosphoramidites needed for solid-phase oligonucleotide synthesis have been reported, and several are commercially available. We report here an efficient synthesis of 3'-monophosphates from 3'-phosphoramidites and the subsequent enzymatic conversion of 3'-monophosphates to the corresponding 5'-monophosphates using commercially available enzymes.
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Affiliation(s)
- Song Zheng
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA
| | - Ai Tran
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA
| | - Alyson M Curry
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA.
| | - Dawanna S White
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA.
| | - Yana Cen
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA. and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
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35
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Sui C, Wang Q, Zhou Y, Zhang D, Yin H, Ai S. Homogeneous detection of 5-hydroxymethylcytosine based on electrochemiluminescence quenching of g-C 3N 4/MoS 2 nanosheets by ferrocenedicarboxylic acid polymer. Talanta 2020; 219:121211. [PMID: 32887114 DOI: 10.1016/j.talanta.2020.121211] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/18/2020] [Accepted: 05/21/2020] [Indexed: 01/02/2023]
Abstract
A sensitively homogeneous electrochemiluminescence (ECL) method was developed for 5-hydroxymethylcytosine (5hmC) detection using TiO2/MoS2/g-C3N4/GCE as substrate electrode, where g-C3N4 was employed as the ECL active material, the MoS2 nanosheets were used as co-catalyst, and TiO2 was adopted as phosphate group capture reagent. To achieve the specific recognition and capture of 5hmC, the covalent reaction between -CH2OH and -SH was employed under the catalysis of HhaI methyltransferase, in which, -SH functionalized ferrocenedicarboxylic acid polymer (PFc-SH) was prepared as 5hmC capture reagent and ECL signal quencher. Then, based on the interaction between TiO2 and phosphate group of 5hmC, the target was recognized and captured on electrode, resulting in a decreased ECL response due to the quenching effect of PFc-SH. Under optimal conditions, the biosensor presented the linear range from 0.01 to 500 nM with the detection limit of 3.21 pM (S/N = 3). The steric effect on electrode surface is a bottle-neck issue restricting devised biosensors advancement. In this work, the reaction between 5hmC and PFc was carried out in the solution, which can avoid steric effect on electrode surface to keep the high activity of enzyme. In addition, the biosensor was successfully applied to detect 5hmC in genomic DNA of chicken embryo fibroblast cells and different tissues of rice seedlings.
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Affiliation(s)
- Chengji Sui
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Qian Wang
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Yunlei Zhou
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China.
| | - Dingding Zhang
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Huanshun Yin
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China.
| | - Shiyun Ai
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
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36
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Schön A, Kaminska E, Schelter F, Ponkkonen E, Korytiaková E, Schiffers S, Carell T. Analyse des aktiven Deformylierungsmechanismus von 5‐Formyl‐2′‐Desoxycytidin in Stammzellen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000414] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Alexander Schön
- Department of Chemistry Ludwig-Maximilians Universität München Butenandtstr. 5–13 81377 München Deutschland
| | - Ewelina Kaminska
- Department of Chemistry Ludwig-Maximilians Universität München Butenandtstr. 5–13 81377 München Deutschland
| | - Florian Schelter
- Department of Chemistry Ludwig-Maximilians Universität München Butenandtstr. 5–13 81377 München Deutschland
| | - Eveliina Ponkkonen
- Department of Chemistry Ludwig-Maximilians Universität München Butenandtstr. 5–13 81377 München Deutschland
| | - Eva Korytiaková
- Department of Chemistry Ludwig-Maximilians Universität München Butenandtstr. 5–13 81377 München Deutschland
| | - Sarah Schiffers
- Department of Chemistry Ludwig-Maximilians Universität München Butenandtstr. 5–13 81377 München Deutschland
| | - Thomas Carell
- Department of Chemistry Ludwig-Maximilians Universität München Butenandtstr. 5–13 81377 München Deutschland
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37
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Schön A, Kaminska E, Schelter F, Ponkkonen E, Korytiaková E, Schiffers S, Carell T. Analysis of an Active Deformylation Mechanism of 5-Formyl-deoxycytidine (fdC) in Stem Cells. Angew Chem Int Ed Engl 2020; 59:5591-5594. [PMID: 31999041 PMCID: PMC7155088 DOI: 10.1002/anie.202000414] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Indexed: 11/30/2022]
Abstract
The removal of 5‐methyl‐deoxycytidine (mdC) from promoter elements is associated with reactivation of the silenced corresponding genes. It takes place through an active demethylation process involving the oxidation of mdC to 5‐hydroxymethyl‐deoxycytidine (hmdC) and further on to 5‐formyl‐deoxycytidine (fdC) and 5‐carboxy‐deoxycytidine (cadC) with the help of α‐ketoglutarate‐dependent Tet oxygenases. The next step can occur through the action of a glycosylase (TDG), which cleaves fdC out of the genome for replacement by dC. A second pathway is proposed to involve C−C bond cleavage that converts fdC directly into dC. A 6‐aza‐5‐formyl‐deoxycytidine (a‐fdC) probe molecule was synthesized and fed to various somatic cell lines and induced mouse embryonic stem cells, together with a 2′‐fluorinated fdC analogue (F‐fdC). While deformylation of F‐fdC was clearly observed in vivo, it did not occur with a‐fdC, thus suggesting that the C−C bond‐cleaving deformylation is initiated by nucleophilic activation.
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Affiliation(s)
- Alexander Schön
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Ewelina Kaminska
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Florian Schelter
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Eveliina Ponkkonen
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Eva Korytiaková
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Sarah Schiffers
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377, München, Germany
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38
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Bhavsar-Jog YP, Van Dornshuld E, Brooks TA, Tschumper GS, Wadkins RM. Co-Localization of DNA i-Motif-Forming Sequences and 5-Hydroxymethyl-cytosines in Human Embryonic Stem Cells. Molecules 2019; 24:molecules24193619. [PMID: 31597270 PMCID: PMC6804057 DOI: 10.3390/molecules24193619] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/01/2019] [Accepted: 10/04/2019] [Indexed: 12/25/2022] Open
Abstract
G-quadruplexes (G4s) and i-motifs (iMs) are tetraplex DNA structures. Sequences capable of forming G4/iMs are abundant near the transcription start sites (TSS) of several genes. G4/iMs affect gene expression in vitro. Depending on the gene, the presence of G4/iMs can enhance or suppress expression, making it challenging to discern the underlying mechanism by which they operate. Factors affecting G4/iM structures can provide additional insight into their mechanism of regulation. One such factor is epigenetic modification. The 5-hydroxymethylated cytosines (5hmCs) are epigenetic modifications that occur abundantly in human embryonic stem cells (hESC). The 5hmCs, like G4/iMs, are known to participate in gene regulation and are also enriched near the TSS. We investigated genomic co-localization to assess the possibility that these two elements may play an interdependent role in regulating genes in hESC. Our results indicate that amongst 15,760 G4/iM-forming locations, only 15% have 5hmCs associated with them. A detailed analysis of G4/iM-forming locations enriched in 5hmC indicates that most of these locations are in genes that are associated with cell differentiation, proliferation, apoptosis and embryogenesis. The library generated from our analysis is an important resource for investigators exploring the interdependence of these DNA features in regulating expression of selected genes in hESC.
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Affiliation(s)
- Yogini P Bhavsar-Jog
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA.
| | - Eric Van Dornshuld
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Tracy A Brooks
- Department of Pharmaceutical Sciences, Binghamton University, Binghamton, NY 13902, USA.
| | - Gregory S Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA.
| | - Randy M Wadkins
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA.
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39
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Photoelectrochemical biosensor for 5hmC detection based on the photocurrent inhibition effect of ZnO on MoS2/C3N4 heterojunction. Biosens Bioelectron 2019; 142:111516. [DOI: 10.1016/j.bios.2019.111516] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/05/2019] [Accepted: 07/13/2019] [Indexed: 12/19/2022]
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40
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Kavoosi S, Sudhamalla B, Dey D, Shriver K, Arora S, Sappa S, Islam K. Site- and degree-specific C-H oxidation on 5-methylcytosine homologues for probing active DNA demethylation. Chem Sci 2019; 10:10550-10555. [PMID: 32055378 PMCID: PMC6988753 DOI: 10.1039/c9sc02629k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/28/2019] [Indexed: 12/14/2022] Open
Abstract
Activity of TET, AID and TDG enzymes in the DNA demethylation pathway was controlled using stereoelectronically constrained 5-methylcytosine homologues to generate conditionally stable DNA modification.
Ten-eleven translocation (TET) enzymes oxidize C–H bonds in 5-methylcytosine (5mC) to hydroxyl (5hmC), formyl (5fC) and carboxyl (5caC) intermediates en route to DNA demethylation. It has remained a challenge to study the function of a single oxidized product. We investigate whether alkyl groups other than methyl could be oxidized by TET proteins to generate a specific intermediate. We report here that TET2 oxidizes 5-ethylcytosine (5eC) only to 5-hydroxyethylcytosine (5heC). In biochemical assays, 5heC acts as a docking site for proteins implicated in transcription, imbuing this modification with potential gene regulatory activity. We observe that 5heC is resistant to downstream wild type hydrolases, but not to the engineered enzymes, thus establishing a unique tool to conditionally alter the stability of 5heC on DNA. Furthermore, we devised a chemical approach for orthogonal labeling of 5heC. Our work offers a platform for synthesis of novel 5-alkylcytosines, provides an approach to ‘tame’ TET activity, and identifies 5heC as an unnatural modification with a potential to control chromatin-dependent processes.
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Affiliation(s)
- Sam Kavoosi
- Department of Chemistry , University of Pittsburgh , Pennsylvania 15260 , USA .
| | - Babu Sudhamalla
- Department of Chemistry , University of Pittsburgh , Pennsylvania 15260 , USA .
| | - Debasis Dey
- Department of Chemistry , University of Pittsburgh , Pennsylvania 15260 , USA .
| | - Kirsten Shriver
- Department of Chemistry , University of Pittsburgh , Pennsylvania 15260 , USA .
| | - Simran Arora
- Department of Chemistry , University of Pittsburgh , Pennsylvania 15260 , USA .
| | - Sushma Sappa
- Department of Chemistry , University of Pittsburgh , Pennsylvania 15260 , USA .
| | - Kabirul Islam
- Department of Chemistry , University of Pittsburgh , Pennsylvania 15260 , USA .
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41
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Wildenhof TM, Schiffers S, Traube FR, Mayer P, Carell T. Influencing Epigenetic Information with a Hydrolytically Stable Carbocyclic 5‐Aza‐2′‐deoxycytidine. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Thomas M. Wildenhof
- Department of Chemistry Ludwig-Maximilians-Universität Butenandtstrasse 5–13 Munich Germany
| | - Sarah Schiffers
- Department of Chemistry Ludwig-Maximilians-Universität Butenandtstrasse 5–13 Munich Germany
| | - Franziska R. Traube
- Department of Chemistry Ludwig-Maximilians-Universität Butenandtstrasse 5–13 Munich Germany
| | - Peter Mayer
- Department of Chemistry Ludwig-Maximilians-Universität Butenandtstrasse 5–13 Munich Germany
| | - Thomas Carell
- Department of Chemistry Ludwig-Maximilians-Universität Butenandtstrasse 5–13 Munich Germany
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42
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Xiong J, Ye TT, Ma CJ, Cheng QY, Yuan BF, Feng YQ. N 6-Hydroxymethyladenine: a hydroxylation derivative of N6-methyladenine in genomic DNA of mammals. Nucleic Acids Res 2019; 47:1268-1277. [PMID: 30517733 PMCID: PMC6379677 DOI: 10.1093/nar/gky1218] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/04/2018] [Accepted: 11/22/2018] [Indexed: 12/19/2022] Open
Abstract
In addition to DNA cytosine methylation (5-methyl-2′-deoxycytidine, m5dC), DNA adenine methylation (N6-methyl-2′-deoxyadenosine, m6dA) is another DNA modification that has been discovered in eukaryotes. Recent studies demonstrated that the content and distribution of m6dA in genomic DNA of vertebrates and mammals exhibit dynamic regulation, indicating m6dA may function as a potential epigenetic mark in DNA of eukaryotes besides m5dC. Whether m6dA undergoes the further oxidation in a similar way to m5dC remains elusive. Here, we reported the existence of a new DNA modification, N6-hydroxymethyl-2′-deoxyadenosine (hm6dA), in genomic DNA of mammalian cells and tissues. We found that hm6dA can be formed from the hydroxylation of m6dA by the Fe2+- and 2-oxoglutarate-dependent ALKBH1 protein in genomic DNA of mammals. In addition, the content of hm6dA exhibited significant increase in lung carcinoma tissues. The increased expression of ALKBH1 in lung carcinoma tissues may contribute to the increase of hm6dA in DNA. Taken together, our study reported the existence and formation of hm6dA in genomic DNA of mammals.
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Affiliation(s)
- Jun Xiong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Tian-Tian Ye
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Cheng-Jie Ma
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Qing-Yun Cheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
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43
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Wildenhof TM, Schiffers S, Traube FR, Mayer P, Carell T. Influencing Epigenetic Information with a Hydrolytically Stable Carbocyclic 5‐Aza‐2′‐deoxycytidine. Angew Chem Int Ed Engl 2019; 58:12984-12987. [DOI: 10.1002/anie.201904794] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/31/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Thomas M. Wildenhof
- Department of Chemistry Ludwig-Maximilians-Universität Butenandtstrasse 5–13 Munich Germany
| | - Sarah Schiffers
- Department of Chemistry Ludwig-Maximilians-Universität Butenandtstrasse 5–13 Munich Germany
| | - Franziska R. Traube
- Department of Chemistry Ludwig-Maximilians-Universität Butenandtstrasse 5–13 Munich Germany
| | - Peter Mayer
- Department of Chemistry Ludwig-Maximilians-Universität Butenandtstrasse 5–13 Munich Germany
| | - Thomas Carell
- Department of Chemistry Ludwig-Maximilians-Universität Butenandtstrasse 5–13 Munich Germany
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44
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Koller G, Zill P, Soyka M, Adorjan K, Weiss C, Kern A, Nguyen-Thien ML, Kamp F, Proebstl L, Krause D, Ruhdorfer S, Bergmann W, Preuss UW. Short-term changes in global methylation and hydroxymethylation during alcohol detoxification. Eur Neuropsychopharmacol 2019; 29:897-903. [PMID: 31133368 DOI: 10.1016/j.euroneuro.2019.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 05/07/2019] [Accepted: 05/11/2019] [Indexed: 12/21/2022]
Abstract
Alcohol dependence is a common public health problem and epigenetics may offer new aspects in understanding the biological and genetic underpinnings and improve treatment of this complex disease. Supposedly, methylation and hydroxymethylation are altered in brain tissues and in synapse-related genes due to chronic alcohol intake and during withdrawal. To assess potential epigenetic changes after cessation of chronic alcohol intake, we compared 23 alcohol-dependent individuals during inpatient alcohol detoxification with 13 carefully matched controls. Blood samples were taken on the day of admission, after one and after two weeks at the end of inpatient treatment. Genome-wide global methylation and global DNA hydroxymethylation were compared across groups. There were significant differences in global methylation across time from admission to one and two weeks of inpatient withdrawal (p < 0.001). These findings were paralleled to changes in global DNA hydroxymethylation across time when age was employed as a cofactor (p < 0.001). Several potentially influencing variables like severity of withdrawal, dose of withdrawal medication and alcohol intake before admission did not yield significant influence on epigenetic changes. The results confirm previous findings of significant alterations of epigenetic patterns during alcohol intoxication and present for the first time hydroxymethylation changes in these individuals.
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Affiliation(s)
- Gabriele Koller
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany.
| | - Peter Zill
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Michael Soyka
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany; Medical Park Chiemseeblick, Bernau am Chiemsee, Germany
| | - Kristina Adorjan
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Claudia Weiss
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Antonia Kern
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Mai-Ly Nguyen-Thien
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Felicia Kamp
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Lisa Proebstl
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Daniela Krause
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Sarah Ruhdorfer
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Wilhelm Bergmann
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Ulrich W Preuss
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany; Vitos-Klinik Psychiatrie und Psychotherapie Herborn, Herborn, Germany
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45
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Rivas MP, Aguiar TFM, Fernandes GR, Caires-Júnior LC, Goulart E, Telles-Silva KA, Cypriano M, de Toledo SRC, Rosenberg C, Carraro DM, da Costa CML, da Cunha IW, Krepischi ACV. TET Upregulation Leads to 5-Hydroxymethylation Enrichment in Hepatoblastoma. Front Genet 2019; 10:553. [PMID: 31249594 PMCID: PMC6582250 DOI: 10.3389/fgene.2019.00553] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/24/2019] [Indexed: 12/14/2022] Open
Abstract
Hepatoblastoma is an embryonal liver tumor carrying few genetic alterations. We previously disclosed in hepatoblastomas a genome-wide methylation dysfunction, characterized by hypermethylation at specific CpG islands, in addition to a low-level hypomethylation pattern in non-repetitive intergenic sequences, in comparison to non-tumoral liver tissues, shedding light into a crucial role for epigenetic dysregulation in this type of cancer. To explore the underlying mechanisms possibly related to aberrant epigenetic modifications, we evaluated the expression profile of a set of genes engaged in the epigenetic machinery related to DNA methylation (DNMT1, DNMT3A, DNMT3B, DNMT3L, UHRF1, TET1, TET2, and TET3), as well as the 5-hydroxymethylcytosine (5hmC) global level. We observed in hepatoblastomas a general disrupted expression of these genes from the epigenetic machinery, mainly UHRF1, TET1, and TET2 upregulation, in association with an enrichment of 5hmC content. Our findings support a model of active demethylation by TETs in hepatoblastoma, probably during early stages of liver development, which in combination with UHRF1 overexpression would lead to DNA hypomethylation and an increase in overall 5hmC content. Furthermore, our data suggest that decreased 5hmC content might be associated with poor survival rate, highlighting a pivotal role of epigenetics in hepatoblastoma development and progression.
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Affiliation(s)
- Maria Prates Rivas
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Talita Ferreira Marques Aguiar
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.,International Center of Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | | | - Luiz Carlos Caires-Júnior
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ernesto Goulart
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Kayque Alves Telles-Silva
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Monica Cypriano
- Department of Pediatrics, Support Group for Children and Adolescents With Cancer (GRAACC), Federal University of São Paulo, São Paulo, Brazil
| | - Silvia Regina Caminada de Toledo
- Department of Pediatrics, Support Group for Children and Adolescents With Cancer (GRAACC), Federal University of São Paulo, São Paulo, Brazil
| | - Carla Rosenberg
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Dirce Maria Carraro
- International Center of Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | | | | | - Ana Cristina Victorino Krepischi
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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Sui C, Wang T, Zhou Y, Yin H, Meng X, Zhang S, Waterhouse GI, Xu Q, Zhuge Y, Ai S. Photoelectrochemical biosensor for hydroxymethylated DNA detection and T4-β-glucosyltransferase activity assay based on WS2 nanosheets and carbon dots. Biosens Bioelectron 2019; 127:38-44. [DOI: 10.1016/j.bios.2018.11.054] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/26/2018] [Accepted: 11/28/2018] [Indexed: 11/28/2022]
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Deciphering nucleic acid modifications by chemical derivatization-mass spectrometry analysis. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2018.04.021] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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48
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Lai W, Mo J, Yin J, Lyu C, Wang H. Profiling of epigenetic DNA modifications by advanced liquid chromatography-mass spectrometry technologies. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.10.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Li QY, Xie NB, Xiong J, Yuan BF, Feng YQ. Single-Nucleotide Resolution Analysis of 5-Hydroxymethylcytosine in DNA by Enzyme-Mediated Deamination in Combination with Sequencing. Anal Chem 2018; 90:14622-14628. [PMID: 30457326 DOI: 10.1021/acs.analchem.8b04833] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The report of the existence of 5-hydroxymethylcytosine (hm5C) in mammalian genomes is a milestone discovery. hm5C is now generally viewed as the sixth base of DNA with important functions on epigenetic regulation. The in-depth investigation of the biological functions of hm5C requires elucidating the distribution patterns of hm5C in genomes, better in single-nucleotide resolution. It was reported that the cytosine deaminases of the APOBEC (apolipoprotein B mRNA-editing catalytic polypeptide-like) family are nucleic acid editing enzymes and can deaminate cytosine (C) to form uracil (U). Particularly, a subfamily of APOBEC (APOBEC3A) can efficiently deaminate both C and 5-methylcytosine (m5C). In the current study, we identified that APOBEC3A protein can effectively deaminate C, m5C, and hm5C but shows no observable deamination activity toward glycosylated hm5C (β-glucosyl-5-hydroxymethyl-2'-deoxycytidine, ghm5C) by using the restriction enzyme-based assay and liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) analysis. By virtue of the differential deamination activity of APOBEC3A toward C, m5C, and ghm5C in conjugation with sequencing, we developed the single-nucleotide resolution analysis of hm5C in DNA. In this analytical strategy, the original C and m5C in DNA will be deaminated by APOBEC3A to form U and thymine (T), both of which will read as T during sequencing, while ghm5C is resistant to deamination and will read as C during sequencing. Therefore, the remaining C in the sequence context only could come from original hm5C, which offers the single-nucleotide resolution analysis of hm5C in DNA. This APOBEC3A-mediated deamination sequencing (AMD-seq) is straightforward and involves no bisulfite treatment, which avoids the substantial degradation of DNA. Future application of this strategy can be performed for the reliable mapping of hm5C in genome-wide scale at the single-nucleotide resolution.
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Affiliation(s)
- Qiao-Ying Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , People's Republic of China
| | - Neng-Bin Xie
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , People's Republic of China
| | - Jun Xiong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , People's Republic of China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , People's Republic of China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , People's Republic of China
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Navarro-Sánchez L, Águeda-Gómez B, Aparicio S, Pérez-Tur J. Epigenetic Study in Parkinson's Disease: A Pilot Analysis of DNA Methylation in Candidate Genes in Brain. Cells 2018; 7:cells7100150. [PMID: 30261625 PMCID: PMC6210421 DOI: 10.3390/cells7100150] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/15/2018] [Accepted: 09/21/2018] [Indexed: 01/08/2023] Open
Abstract
Efforts have been made to understand the pathophysiology of Parkinson’s disease (PD). A significant number of studies have focused on genetics, despite the fact that the described pathogenic mutations have been observed only in around 10% of patients; this observation supports the fact that PD is a multifactorial disorder. Lately, differences in miRNA expression, histone modification, and DNA methylation levels have been described, highlighting the importance of epigenetic factors in PD etiology. Taking all this into consideration, we hypothesized that an alteration in the level of methylation in PD-related genes could be related to disease pathogenesis, possibly due to alterations in gene expression. After analysing promoter regions of five PD-related genes in three brain regions by pyrosequencing, we observed some differences in DNA methylation levels (hypo and hypermethylation) in substantia nigra in some CpG dinucleotides that, possibly through an alteration in Sp1 binding, could alter their expression.
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Affiliation(s)
- Luis Navarro-Sánchez
- Unitat de Genètica Molecular, Instituto de Biomedicina de Valencia, CSIC, 46010 València, Spain.
| | - Beatriz Águeda-Gómez
- Unitat de Genètica Molecular, Instituto de Biomedicina de Valencia, CSIC, 46010 València, Spain.
| | - Silvia Aparicio
- Unitat de Genètica Molecular, Instituto de Biomedicina de Valencia, CSIC, 46010 València, Spain.
| | - Jordi Pérez-Tur
- Unitat de Genètica Molecular, Instituto de Biomedicina de Valencia, CSIC, 46010 València, Spain.
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), 46010 València, Spain.
- Unidad Mixta de Genética y Neurología, Instituto de Investigación Sanitaria La Fe, 46026 València, Spain.
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