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Ye C, Zhao Z, Lai P, Chen C, Jian F, Liang H, Guo Q. Strategies for the detection of site-specific DNA methylation and its application, opportunities and challenges in the field of electrochemical biosensors. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 39051422 DOI: 10.1039/d4ay00779d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
DNA methylation is an epigenetic modification that plays a crucial role in various biological processes. Aberrant DNA methylation is closely associated with the onset of diseases, and the specific localization of methylation sites in the genome offers further insight into the connection between methylation and diseases. Currently, there are numerous methods available for site-specific methylation detection. Electrochemical biosensors have garnered significant attention due to their distinct advantages, such as rapidity, simplicity, high sensitivity, low cost, and the potential for miniaturization. In this paper, we present a systematic review of the primary sensing strategies utilized in the past decade for analyzing site-specific methylation and their applications in electrochemical sensors, from a novel perspective focusing on the localization analysis of site-specific methylation. These strategies include bisulfite treatment, restriction endonuclease treatment, other sensing strategies, and deamination without direct bisulfite treatment. We hope that this paper can offer ideas and references for establishing site-specific methylation electrochemical analysis in clinical practice.
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Affiliation(s)
- Chenliu Ye
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Zhibin Zhao
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Penghui Lai
- The Second Hospital of Longyan, Longyan 364000, China
| | - Chunmei Chen
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Fumei Jian
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Haiying Liang
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Qiongying Guo
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
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2
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Yan B, Wang D, Ettwiller L. Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine. Genome Res 2024; 34:904-913. [PMID: 38858087 DOI: 10.1101/gr.278294.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
Multiomics require concerted recording of independent information, ideally from a single experiment. In this study, we introduce RIMS-seq2, a high-throughput technique to simultaneously sequence genomes and overlay methylation information while requiring only a small modification of the experimental protocol for high-throughput DNA sequencing to include a controlled deamination step. Importantly, the rate of deamination of 5-methylcytosine is negligible and thus does not interfere with standard DNA sequencing and data processing. Thus, RIMS-seq2 libraries from whole- or targeted-genome sequencing show the same germline variation calling accuracy and sensitivity compared with standard DNA-seq. Additionally, regional methylation levels provide an accurate map of the human methylome.
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Affiliation(s)
- Bo Yan
- New England Biolabs Incorporated, Ipswich, Massachusetts 01938, USA
| | - Duan Wang
- SLC Management, Wellesley Hills, Massachusetts 02481, USA
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3
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Abstract
This review delves into the rapidly evolving landscape of liquid biopsy technologies based on cell-free DNA (cfDNA) and cell-free RNA (cfRNA) and their increasingly prominent role in precision medicine. With the advent of high-throughput DNA sequencing, the use of cfDNA and cfRNA has revolutionized noninvasive clinical testing. Here, we explore the physical characteristics of cfDNA and cfRNA, present an overview of the essential engineering tools used by the field, and highlight clinical applications, including noninvasive prenatal testing, cancer testing, organ transplantation surveillance, and infectious disease testing. Finally, we discuss emerging technologies and the broadening scope of liquid biopsies to new areas of diagnostic medicine.
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Affiliation(s)
- Conor Loy
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA;
| | - Lauren Ahmann
- Department of Pathology, Stanford University, Stanford, California, USA;
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA;
| | - Wei Gu
- Department of Pathology, Stanford University, Stanford, California, USA;
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4
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Fabyanic EB, Hu P, Qiu Q, Berríos KN, Connolly DR, Wang T, Flournoy J, Zhou Z, Kohli RM, Wu H. Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects. Nat Biotechnol 2024; 42:960-974. [PMID: 37640946 DOI: 10.1038/s41587-023-01909-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/19/2023] [Indexed: 08/31/2023]
Abstract
Oxidative modification of 5-methylcytosine (5mC) by ten-eleven translocation (TET) DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of oxidized 5mC. Existing single-cell bisulfite sequencing methods cannot resolve 5mC and 5hmC, leaving the cell-type-specific regulatory mechanisms of TET and 5hmC largely unknown. Here, we present joint single-nucleus (hydroxy)methylcytosine sequencing (Joint-snhmC-seq), a scalable and quantitative approach that simultaneously profiles 5hmC and true 5mC in single cells by harnessing differential deaminase activity of APOBEC3A toward 5mC and chemically protected 5hmC. Joint-snhmC-seq profiling of single nuclei from mouse brains reveals an unprecedented level of epigenetic heterogeneity of both 5hmC and true 5mC at single-cell resolution. We show that cell-type-specific profiles of 5hmC or true 5mC improve multimodal single-cell data integration, enable accurate identification of neuronal subtypes and uncover context-specific regulatory effects on cell-type-specific genes by TET enzymes.
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Affiliation(s)
- Emily B Fabyanic
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Peng Hu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Kiara N Berríos
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel R Connolly
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Tong Wang
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer Flournoy
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhaolan Zhou
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M Kohli
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
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Li T, Cheng C, Liu J. Chemical and Enzyme-Mediated Chemical Reactions for Studying Nucleic Acids and Their Modifications. Chembiochem 2024:e202400220. [PMID: 38742371 DOI: 10.1002/cbic.202400220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/16/2024]
Abstract
Nucleic acids are genetic information-carrying molecules inside cells. Apart from basic nucleotide building blocks, there exist various naturally occurring chemical modifications on nucleobase and ribose moieties, which greatly increase the encoding complexity of nuclei acids, contribute to the alteration of nucleic acid structures, and play versatile regulation roles in gene expression. To study the functions of certain nucleic acids in various biological contexts, robust tools to specifically label and identify these macromolecules and their modifications, and to illuminate their structures are highly necessary. In this review, we summarize recent technique advances of using chemical and enzyme-mediated chemical reactions to study nucleic acids and their modifications and structures. By highlighting the chemical principles of these techniques, we aim to present a perspective on the advancement of the field as well as to offer insights into developing specific chemical reactions and precise enzyme catalysis utilized for nucleic acids and their modifications.
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Affiliation(s)
- Tengwei Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang Province, China
| | - Chongguang Cheng
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang Province, China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang Province, China
- Life Sciences Institute, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang Province, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, 310009, Zhejiang Province, China
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6
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Lee SM. Detecting DNA hydroxymethylation: exploring its role in genome regulation. BMB Rep 2024; 57:135-142. [PMID: 38449301 PMCID: PMC10979348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/15/2024] [Accepted: 02/01/2024] [Indexed: 03/08/2024] Open
Abstract
DNA methylation is one of the most extensively studied epigenetic regulatory mechanisms, known to play crucial roles in various organisms. It has been implicated in the regulation of gene expression and chromatin changes, ranging from global alterations during cell state transitions to locus-specific modifications. 5-hydroxymethylcytosine (5hmC) is produced by a major oxidation, from 5-methylcytosine (5mC), catalyzed by the ten-eleven translocation (TET) enzymes, and is gradually being recognized for its significant role in genome regulation. With the development of state-of-the-art experimental techniques, it has become possible to detect and distinguish 5mC and 5hmC at base resolution. Various techniques have evolved, encompassing chemical and enzymatic approaches, as well as thirdgeneration sequencing techniques. These advancements have paved the way for a thorough exploration of the role of 5hmC across a diverse array of cell types, from embryonic stem cells (ESCs) to various differentiated cells. This review aims to comprehensively report on recent techniques and discuss the emerging roles of 5hmC. [BMB Reports 2024; 57(3): 135-142].
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Affiliation(s)
- Sun-Min Lee
- Department of Physics, Konkuk Univeristy, Seoul 05029, Korea
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7
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Zhu C, Hao Z, Liu D. Reshaping the Landscape of the Genome: Toolkits for Precise DNA Methylation Manipulation and Beyond. JACS AU 2024; 4:40-57. [PMID: 38274248 PMCID: PMC10806789 DOI: 10.1021/jacsau.3c00671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 01/27/2024]
Abstract
DNA methylation plays a pivotal role in various biological processes and is highly related to multiple diseases. The exact functions of DNA methylation are still puzzling due to its uneven distribution, dynamic conversion, and complex interactions with other substances. Current methods such as chemical- and enzyme-based sequencing techniques have enabled us to pinpoint DNA methylation at single-base resolution, which necessitated the manipulation of DNA methylation at comparable resolution to precisely illustrate the correlations and causal relationships between the functions of DNA methylation and its spatiotemporal patterns. Here a perspective on the past, recent process, and future of precise DNA methylation tools is provided. Specifically, genome-wide and site-specific manipulation of DNA methylation methods is discussed, with an emphasis on their principles, limitations, applications, and future developmental directions.
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Affiliation(s)
- Chenyou Zhu
- Engineering
Research Center of Advanced Rare Earth Materials, Ministry of Education,
Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ziyang Hao
- School
of Pharmaceutical Sciences, Capital Medical
University, Beijing, 100069, PR China
| | - Dongsheng Liu
- Engineering
Research Center of Advanced Rare Earth Materials, Ministry of Education,
Department of Chemistry, Tsinghua University, Beijing 100084, China
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Torban E, Goodyer P. Wilms' tumor gene 1: lessons from the interface between kidney development and cancer. Am J Physiol Renal Physiol 2024; 326:F3-F19. [PMID: 37916284 DOI: 10.1152/ajprenal.00248.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023] Open
Abstract
In 1990, mutations of the Wilms' tumor-1 gene (WT1), encoding a transcription factor in the embryonic kidney, were found in 10-15% of Wilms' tumors; germline WT1 mutations were associated with hereditary syndromes involving glomerular and reproductive tract dysplasia. For more than three decades, these discoveries prompted investigators to explore the embryonic role of WT1 and the mechanisms by which loss of WT1 leads to malignant transformation. Here, we discuss how alternative splicing of WT1 generates isoforms that act in a context-specific manner to activate or repress target gene transcription. WT1 also regulates posttranscriptional regulation, alters the epigenetic landscape, and activates miRNA expression. WT1 functions at multiple stages of kidney development, including the transition from resting stem cells to committed nephron progenitor, which it primes to respond to WNT9b signals from the ureteric bud. WT1 then drives nephrogenesis by activating WNT4 expression and directing the development of glomerular podocytes. We review the WT1 mutations that account for Denys-Drash syndrome, Frasier syndrome, and WAGR syndrome. Although the WT1 story began with Wilms' tumors, an understanding of the pathways that link aberrant kidney development to malignant transformation still has some important gaps. Loss of WT1 in nephrogenic rests may leave these premalignant clones with inadequate DNA repair enzymes and may disturb the epigenetic landscape. Yet none of these observations provide a complete picture of Wilms' tumor pathogenesis. It appears that the WT1 odyssey is unfinished and still holds a great deal of untilled ground to be explored.
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Affiliation(s)
- Elena Torban
- Department of Medicine, McGill University and Research Institute of McGill University Health Center, Montreal, Quebec, Canada
| | - Paul Goodyer
- Department of Human Genetics, Montreal Children's Hospital and McGill University, Montreal, Quebec, Canada
- Department of Pediatrics, Montreal Children's Hospital and McGill University, Montreal, Quebec, Canada
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9
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Loo CE, Hix MA, Wang T, Cisneros GA, Kohli RM. Revealing Drivers for Carboxy- S-adenosyl-l-methionine Use by Neomorphic Variants of a DNA Methyltransferase. ACS Chem Biol 2023; 18:2224-2232. [PMID: 37379458 PMCID: PMC10592258 DOI: 10.1021/acschembio.3c00184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Methylation of DNA plays a key role in diverse biological processes spanning from bacteria to mammals. DNA methyltransferases (MTases) typically employ S-adenosyl-l-methionine (SAM) as a critical cosubstrate and the relevant methyl donor for modification of the C5 position of cytosine. Recently, work on the CpG-specific bacterial MTase, M.MpeI, has shown that a single N374K point mutation can confer the enzyme with the neomorphic ability to use the sparse, naturally occurring metabolite carboxy-S-adenosyl-l-methionine (CxSAM) in order to generate the unnatural DNA modification, 5-carboxymethylcytosine (5cxmC). Here, we aimed to investigate the mechanistic basis for this DNA carboxymethyltransferase (CxMTase) activity by employing a combination of computational modeling and in vitro characterization. Modeling of substrate interactions with the enzyme variant allowed us to identify a favorable salt bridge between CxSAM and N374K that helps to rationalize selectivity of the CxMTase. Unexpectedly, we also discovered a potential role for a key active site E45 residue that makes a bidentate interaction with the ribosyl sugar of CxSAM, located on the opposite face of the CxMTase active site. Prompted by these modeling results, we further explored the space-opening E45D mutation and found that the E45D/N374K double mutant in fact inverts selectivity, preferring CxSAM over SAM in biochemical assays. These findings provide new insight into CxMTase active site architecture and may offer broader utility given the numerous opportunities offered by using SAM analogs for selective molecular labeling in concert with nucleic acid or even protein-modifying MTases.
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Affiliation(s)
- Christian E. Loo
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Mark A. Hix
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Tong Wang
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - G. Andrés Cisneros
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75801, United States; Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75801, United States
| | - Rahul M. Kohli
- Department of Medicine and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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10
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Abakir A, Reik W. Direct methylation sequencing. Nat Chem Biol 2023:10.1038/s41589-023-01356-9. [PMID: 37322154 DOI: 10.1038/s41589-023-01356-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Affiliation(s)
- Abdulkadir Abakir
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge, UK.
| | - Wolf Reik
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge, UK
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome Trust, Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
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