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Cheng Y, Chen C, Wang F, Chen Z. A highly sensitive signal-on biosensor based on restriction enzyme-mediated molecular switch for detection of TET1. Bioelectrochemistry 2023; 152:108433. [PMID: 37031472 DOI: 10.1016/j.bioelechem.2023.108433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/07/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023]
Abstract
Ten-eleven translocation 1 (TET1) is a member of the TET enzyme family of dioxygenases, which plays an important role in active DNA demethylation. Therefore, the sensitive TET1 detection could help us better understand DNA methylation-demethylation in epigenetics. Here we report a detection method that consists of electrode fabrication, TET1 modification, DNA digestion, signal-on oxidoreduction, and current peak monitoring. An exquisitely designed 5'end-G-rich oligodeoxynucleotide was synthesized bearing a methylated cytosine (5-mC), which formed into hairpin dsDNA with the MspI recognition sequence (CmCGG/GGCC). Then hairpin dsDNA was fabricated onto gold nanoparticles modified glassy carbon electrode (DNA/AuNPs/GCE) via Au-S bond. The combination uses of restriction enzyme MspI and hemin converted fabricated-dsDNA into peroxidase-mimicking DNAzyme, thereby promoting the reduction of H2O2 with a current peak. However, the current peak was extremely decreased once TET1 and T4 β-GT were used in advance. We confirmed a delicately linear relationship matching between the current difference and TET1 activity from 0.7 to 10.5 ng μL-1 with a detection limit of 0.027 ng μL-1, which outcompeted the former methods at least one order of magnitudes. The TET1 activity evaluation in the existence of Bobcat339 was also tested as the proof of concept of inhibitors screening. Our strategy provides a novel, label-free, and sensitive electrochemical approach that enables us to complete both TET1 activity evaluation and potential TET1 inhibitors screening.
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2
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Dynamic changes in genomic 5-hydroxymethyluracil and N6-methyladenine levels in the Drosophila melanogaster life cycle and in response to different temperature conditions. Sci Rep 2022; 12:17552. [PMID: 36266436 PMCID: PMC9584883 DOI: 10.1038/s41598-022-22490-9] [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: 07/19/2022] [Accepted: 10/14/2022] [Indexed: 01/13/2023] Open
Abstract
In this study, the level of DNA modifications was investigated in three developmental stages of Drosophila melanogaster (larvae, pupae, imago) and in an in vitro model (Schneider 2 cells). Analysis was carried out using two-dimensional ultra-performance liquid chromatography with tandem mass spectrometry. Our method made it possible, for the first time, to analyze a broad spectrum of DNA modifications in the three stages of Drosophila. Each stage was characterized by a specific modification pattern, and the levels of these compounds fluctuated throughout the D. melanogaster life cycle. The level of DNA modification was also compared between insects bred at 25 °C (optimal temperature) and at 18 °C, and the groups differed significantly. The profound changes in N6-methyladenine and 5-hydroxymethyluracil levels during the Drosophila life cycle and as a result of breeding temperature changes indicate that these DNA modifications can play important regulatory roles in response to environmental changes and/or biological conditions. Moreover, the supplementation of Schneider 2 cells with 1 mM L-ascorbic acid caused a time-dependent increase in the level of 5-(hydroxymethyl)-2'-deoxyuridine. These data suggest that a certain pool of this compound may arise from the enzymatic activity of the dTET protein.
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3
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Baljinnyam T, Sowers ML, Hsu CW, Conrad JW, Herring JL, Hackfeld LC, Sowers LC. Chemical and enzymatic modifications of 5-methylcytosine at the intersection of DNA damage, repair, and epigenetic reprogramming. PLoS One 2022; 17:e0273509. [PMID: 36037209 PMCID: PMC9423628 DOI: 10.1371/journal.pone.0273509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 08/09/2022] [Indexed: 11/19/2022] Open
Abstract
The DNA of all living organisms is persistently damaged by endogenous reactions including deamination and oxidation. Such damage, if not repaired correctly, can result in mutations that drive tumor development. In addition to chemical damage, recent studies have established that DNA bases can be enzymatically modified, generating many of the same modified bases. Irrespective of the mechanism of formation, modified bases can alter DNA-protein interactions and therefore modulate epigenetic control of gene transcription. The simultaneous presence of both chemically and enzymatically modified bases in DNA suggests a potential intersection, or collision, between DNA repair and epigenetic reprogramming. In this paper, we have prepared defined sequence oligonucleotides containing the complete set of oxidized and deaminated bases that could arise from 5-methylcytosine. We have probed these substrates with human glycosylases implicated in DNA repair and epigenetic reprogramming. New observations reported here include: SMUG1 excises 5-carboxyuracil (5caU) when paired with A or G. Both TDG and MBD4 cleave 5-formyluracil and 5caU when mispaired with G. Further, TDG not only removes 5-formylcytosine and 5-carboxycytosine when paired with G, but also when mispaired with A. Surprisingly, 5caU is one of the best substrates for human TDG, SMUG1 and MBD4, and a much better substrate than T. The data presented here introduces some unexpected findings that pose new questions on the interactions between endogenous DNA damage, repair, and epigenetic reprogramming pathways.
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Affiliation(s)
- Tuvshintugs Baljinnyam
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Mark L. Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- MD-PhD Combined Degree Program, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Chia Wei Hsu
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- MD-PhD Combined Degree Program, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - James W. Conrad
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jason L. Herring
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Linda C. Hackfeld
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Lawrence C. Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
- * E-mail:
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Recent Advances on DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:295-315. [DOI: 10.1007/978-3-031-11454-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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5
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Assay for TET1 activity and its inhibitors screening with signal amplification by both nanoparticles and Ru(III) redox recycling. J Pharm Biomed Anal 2021; 203:114228. [PMID: 34182409 DOI: 10.1016/j.jpba.2021.114228] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/07/2021] [Accepted: 06/19/2021] [Indexed: 12/14/2022]
Abstract
Ten-eleven translocation protein 1 (TET1) is one member of TET proteins family which plays a key role in dynamic DNA methylation-demethylation process. Herein, a novel biosensor was constructed for TET1 detection and its inhibitors screening utilizing restriction digestion of endonuclease enzyme MspI. Half-methylated oligonucleotide (5mC DNA) was used as target and Ru(NH3)63+ as electrochemical signal probe. After the treatment by TET1 and T4 β-glucosyltransferase (T4 β-GT), target oligonucleotide would not be recognized and digested. If there was no TET1, the target would be digested and the response of biosensor decreased greatly. The current difference of biosensor with and without the incubation with TET1 was therefore dependent on the concentration of TET1. To increase sensitivity of the biosensor, nanostructured film at electrode surface and nanoparticles modified oligonucleotides were employed as signal amplification elements for Ru(NH3)63+ recycling. Finally, this biosensor showed high performance with a wide linear range of TET1 concentration from 3.5-21 ng/μL and a low detection limit of 0.33 ng/μL, which is superior to other existing methods. The inhibition effects of Bobcat339 on TET1 was successfully proved by our biosensor with an IC50 of 38 μM. Not only that, but the feasibility of the biosensor for inhibitors screening was evaluated and further confirmed by other compounds including two anticancer drugs and three active ingredients of traditional Chinese medicine.
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Phage-encoded ten-eleven translocation dioxygenase (TET) is active in C5-cytosine hypermodification in DNA. Proc Natl Acad Sci U S A 2021; 118:2026742118. [PMID: 34155108 PMCID: PMC8256090 DOI: 10.1073/pnas.2026742118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Chemical tailoring of canonical bases expands the functionality of DNA in the same manner that posttranscriptional and -translational modifications enhance functional diversity in RNA and proteins. We describe the activities of ten-eleven translocation dioxygenase (TET)-like iron(II)- and 2-oxo-glutarate–dependent 5mC dioxygenases that are encoded by several bacteriophages to enable hypermodification of C5-methyl cytosine bases in their DNA. Phage TETs act on methylation marks deposited within GpC sequences by functionally-associated cytosine 5-methyltransferases. The hydroxymethyl groups installed are further elaborated by tailoring enzymes, thereby decorating the phage DNA with diverse, complex modifications. These modifications are predicted to have protective roles against host defenses during viral infection. TET/JBP (ten-eleven translocation/base J binding protein) enzymes are iron(II)- and 2-oxo-glutarate–dependent dioxygenases that are found in all kingdoms of life and oxidize 5-methylpyrimidines on the polynucleotide level. Despite their prevalence, few examples have been biochemically characterized. Among those studied are the metazoan TET enzymes that oxidize 5-methylcytosine in DNA to hydroxy, formyl, and carboxy forms and the euglenozoa JBP dioxygenases that oxidize thymine in the first step of base J biosynthesis. Both enzymes have roles in epigenetic regulation. It has been hypothesized that all TET/JBPs have their ancestral origins in bacteriophages, but only eukaryotic orthologs have been described. Here we demonstrate the 5mC-dioxygenase activity of several phage TETs encoded within viral metagenomes. The clustering of these TETs in a phylogenetic tree correlates with the sequence specificity of their genomically cooccurring cytosine C5-methyltransferases, which install the methyl groups upon which TETs operate. The phage TETs favor Gp5mC dinucleotides over the 5mCpG sites targeted by the eukaryotic TETs and are found within gene clusters specifying complex cytosine modifications that may be important for DNA packaging and evasion of host restriction.
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DeNizio JE, Dow BJ, Serrano JC, Ghanty U, Drohat AC, Kohli RM. TET-TDG Active DNA Demethylation at CpG and Non-CpG Sites. J Mol Biol 2021; 433:166877. [PMID: 33561435 DOI: 10.1016/j.jmb.2021.166877] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/02/2021] [Indexed: 11/24/2022]
Abstract
In mammalian genomes, cytosine methylation occurs predominantly at CG (or CpG) dinucleotide contexts. As part of dynamic epigenetic regulation, 5-methylcytosine (mC) can be erased by active DNA demethylation, whereby ten-eleven translocation (TET) enzymes catalyze the stepwise oxidation of mC to 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxycytosine (caC), thymine DNA glycosylase (TDG) excises fC or caC, and base excision repair yields unmodified cytosine. In certain cell types, mC is also enriched at some non-CG (or CH) dinucleotides, however hmC is not. To provide biochemical context for the distribution of modified cytosines observed in biological systems, we systematically analyzed the activity of human TET2 and TDG for substrates in CG and CH contexts. We find that while TET2 oxidizes mC more efficiently in CG versus CH sites, this context preference can be diminished for hmC oxidation. Remarkably, TDG excision of fC and caC is only modestly dependent on CG context, contrasting its strong context dependence for thymine excision. We show that collaborative TET-TDG oxidation-excision activity is only marginally reduced for CA versus CG contexts. Our findings demonstrate that the TET-TDG-mediated demethylation pathway is not limited to CG sites and suggest a rationale for the depletion of hmCH in genomes rich in mCH.
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Affiliation(s)
- Jamie E DeNizio
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, Philadelphia, PA 19147, USA; Department of Medicine, Department of Biochemistry & Biophysics, Perelman School of Medicine, Philadelphia, PA 19147, USA
| | - Blaine J Dow
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Juan C Serrano
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, Philadelphia, PA 19147, USA; Department of Medicine, Department of Biochemistry & Biophysics, Perelman School of Medicine, Philadelphia, PA 19147, USA
| | - Uday Ghanty
- Department of Medicine, Department of Biochemistry & Biophysics, Perelman School of Medicine, Philadelphia, PA 19147, USA
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Rahul M Kohli
- Department of Medicine, Department of Biochemistry & Biophysics, Perelman School of Medicine, Philadelphia, PA 19147, USA.
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Yu Z, Chen X, Cheng Y, Yang H, Wang F, Chen Z. Novel label-free electrochemical strategy for sensitive determination of ten-eleven translocation protein 1. Anal Chim Acta 2021; 1146:140-145. [DOI: 10.1016/j.aca.2020.11.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/07/2020] [Accepted: 11/13/2020] [Indexed: 12/18/2022]
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Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely used technique in the global analysis of epigenetic DNA modifications. The high-resolution chromatographic separation along with sensitive MS detection permits the identification and quantification of deoxyribonucleosides with precision and reliability. Although there have been tremendous advances in LC and MS instrumentation in recent years, sample preparation has not experienced a similar rate of development and is often a bottleneck to chemical analysis. Here we present a protocol for identification and quantification of cytosine modifications that combines a robust and efficient method to generate single nucleosides from genomic DNA samples followed by direct LC-MS/MS analysis.
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Chen X, Cheng Y, Wang Y, Tang J, Wang F, Chen Z. Fluorescence assay based on the thioflavin T-induced conformation switch of G-quadruplexes for TET1 detection. Analyst 2021; 146:2126-2130. [DOI: 10.1039/d1an00109d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A simple and label-free fluorescence method is developed for the highly sensitive detection of TET1 based on ThT/G-quadruplexes in combination with the specific design of oligonucleotides.
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Affiliation(s)
- Xue Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery
- Ministry of Education
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals
- and Wuhan University School of Pharmaceutical Sciences
- Wuhan
| | - Ying Cheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery
- Ministry of Education
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals
- and Wuhan University School of Pharmaceutical Sciences
- Wuhan
| | - Yafen Wang
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biochemical Polymers of Ministry of Education. The Institute for Advanced Studies
- Hubei Province Key Laboratory of Allergy and Immunology
- Wuhan University
- Wuhan
| | - Jing Tang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery
- Ministry of Education
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals
- and Wuhan University School of Pharmaceutical Sciences
- Wuhan
| | - Fang Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery
- Ministry of Education
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals
- and Wuhan University School of Pharmaceutical Sciences
- Wuhan
| | - Zilin Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery
- Ministry of Education
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals
- and Wuhan University School of Pharmaceutical Sciences
- Wuhan
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11
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Tomkuvienė M, Ikasalaitė D, Slyvka A, Rukšėnaitė A, Ravichandran M, Jurkowski TP, Bochtler M, Klimašauskas S. Enzymatic Hydroxylation and Excision of Extended 5-Methylcytosine Analogues. J Mol Biol 2020; 432:6157-6167. [PMID: 33065111 PMCID: PMC7763475 DOI: 10.1016/j.jmb.2020.10.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 11/28/2022]
Abstract
Methylation of cytosine to 5-methylcytosine (mC) is a prevalent reversible epigenetic mark in vertebrates established by DNA methyltransferases (MTases); the methylation mark can be actively erased via a multi-step demethylation mechanism involving oxidation by Ten-eleven translocation (TET) enzyme family dioxygenases, excision of the latter oxidation products by thymine DNA (TDG) or Nei-like 1 (NEIL1) glycosylases followed by base excision repair to restore the unmodified state. Here we probed the activity of the mouse TET1 (mTET1) and Naegleria gruberi TET (nTET) oxygenases with DNA substrates containing extended derivatives of the 5-methylcytosine carrying linear carbon chains and adjacent unsaturated CC bonds. We found that the nTET and mTET1 enzymes were active on modified mC residues in single-stranded and double-stranded DNA in vitro, while the extent of the reactions diminished with the size of the extended group. Iterative rounds of nTET hydroxylations of ssDNA proceeded with high stereo specificity and included not only the natural alpha position but also the adjoining carbon atom in the extended side chain. The regioselectivity of hydroxylation was broken when the reactive carbon was adjoined with an sp1 or sp2 system. We also found that NEIL1 but not TDG was active with bulky TET-oxidation products. These findings provide important insights into the mechanism of these biologically important enzymatic reactions.
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Affiliation(s)
- Miglė Tomkuvienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Diana Ikasalaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Anton Slyvka
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Audronė Rukšėnaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | | | | | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland; Polish Academy of Sciences, Institute of Biochemistry and Biophysics, 02-106 Warsaw, Poland
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania.
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Chen F, Xue J, Zhang J, Bai M, Yu X, Fan C, Zhao Y. Differentiated Visualization of Single-Cell 5-Hydroxymethylpyrimidines with Microfluidic Hydrogel Encoding. J Am Chem Soc 2020; 142:2889-2896. [PMID: 31986025 DOI: 10.1021/jacs.9b11393] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
5-Hydroxymethyluracil ( 5hmU ) is found in the genomes of a diverse range of organisms as another kind of 5-hydroxymethylpyrimidine, with the exception of 5-hydroxymethylcytosine ( 5hmC ). The biological function of 5hmU has not been well explored due to lacking both specific 5hmU recognition and single-cell analysis methods. Here we report differentiated visualization of single-cell 5hmU and 5hmC with microfluidic hydrogel encoding (sc 5hmU / 5hmC -microgel). Single cells and their genomic DNA after cell lysis can be encapsulated in individual agarose microgels. The 5hmU sites are then specifically labeled with thiophosphate for the first time, followed by labeling 5hmC with azide glucose. These labeled bases are each encoded into respective DNA barcode primers by chemical cross-linking. In situ amplification is triggered for single-molecule fluorescence visualization of single-cell 5hmU and 5hmC . On the basis of the sc 5hmU / 5hmC -microgel, we reveal cell type-specific molecular signatures of these two bases with remarkable single-cell heterogeneity. Utilizing machine learning algorithms to decode four-dimensional signatures of 5hmU / 5hmC , we visualize the discrimination of nontumorigenic, carcinoma and highly invasive breast cell lines. This strategy provides a new route to analyze and decode single-cell DNA epigenetic modifications.
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Affiliation(s)
- Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China
| | - Jing Xue
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China
| | - Jin Zhang
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China
| | - Min Bai
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China
| | - Xu Yu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China
| | - Chunhai Fan
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and School of Chemistry and ChemicalEngineering , Shanghai Jiao Tong University , Shanghai 200127 , P. R. China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China
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13
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Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang Y, Zhang X, Blumenthal RM, Cheng X. Structural basis for effects of CpA modifications on C/EBPβ binding of DNA. Nucleic Acids Res 2019; 47:1774-1785. [PMID: 30566668 PMCID: PMC6393304 DOI: 10.1093/nar/gky1264] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/28/2018] [Accepted: 12/08/2018] [Indexed: 12/30/2022] Open
Abstract
CCAAT/enhancer binding proteins (C/EBPs) regulate gene expression in a variety of cells/tissues/organs, during a range of developmental stages, under both physiological and pathological conditions. C/EBP-related transcription factors have a consensus binding specificity of 5'-TTG-CG-CAA-3', with a central CpG/CpG and two outer CpA/TpG dinucleotides. Methylation of the CpG and CpA sites generates a DNA element with every pyrimidine having a methyl group in the 5-carbon position (thymine or 5-methylcytosine (5mC)). To understand the effects of both CpG and CpA modification on a centrally-important transcription factor, we show that C/EBPβ binds the methylated 8-bp element with modestly-increased (2.4-fold) binding affinity relative to the unmodified cognate sequence, while cytosine hydroxymethylation (particularly at the CpA sites) substantially decreased binding affinity (36-fold). The structure of C/EBPβ DNA binding domain in complex with methylated DNA revealed that the methyl groups of the 5mCpA/TpG make van der Waals contacts with Val285 in C/EBPβ. Arg289 recognizes the central 5mCpG by forming a methyl-Arg-G triad, and its conformation is constrained by Val285 and the 5mCpG methyl group. We substituted Val285 with Ala (V285A) in an Ala-Val dipeptide, to mimic the conserved Ala-Ala in many members of the basic leucine-zipper family of transcription factors, important in gene regulation, cell proliferation and oncogenesis. The V285A variant demonstrated a 90-fold binding preference for methylated DNA (particularly 5mCpA methylation) over the unmodified sequence. The smaller side chain of Ala285 permits Arg289 to adopt two alternative conformations, to interact in a similar fashion with either the central 5mCpG or the TpG of the opposite strand. Significantly, the best-studied cis-regulatory elements in RNA polymerase II promoters and enhancers have variable sequences corresponding to the central CpG or reduced to a single G:C base pair, but retain a conserved outer CpA sequence. Our analyses suggest an important modification-dependent CpA recognition by basic leucine-zipper transcription factors.
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Affiliation(s)
- Jie Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dongxue Wang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ren Ren
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jia Li
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Deqiang Sun
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Liu Y, Siejka-Zielińska P, Velikova G, Bi Y, Yuan F, Tomkova M, Bai C, Chen L, Schuster-Böckler B, Song CX. Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution. Nat Biotechnol 2019; 37:424-429. [PMID: 30804537 DOI: 10.1038/s41587-019-0041-2] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 01/22/2019] [Indexed: 02/07/2023]
Abstract
Bisulfite sequencing has been the gold standard for mapping DNA modifications including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) for decades1-4. However, this harsh chemical treatment degrades the majority of the DNA and generates sequencing libraries with low complexity2,5,6. Here, we present a bisulfite-free and base-level-resolution sequencing method, TET-assisted pyridine borane sequencing (TAPS), for detection of 5mC and 5hmC. TAPS combines ten-eleven translocation (TET) oxidation of 5mC and 5hmC to 5-carboxylcytosine (5caC) with pyridine borane reduction of 5caC to dihydrouracil (DHU). Subsequent PCR converts DHU to thymine, enabling a C-to-T transition of 5mC and 5hmC. TAPS detects modifications directly with high sensitivity and specificity, without affecting unmodified cytosines. This method is nondestructive, preserving DNA fragments over 10 kilobases long. We applied TAPS to the whole-genome mapping of 5mC and 5hmC in mouse embryonic stem cells and show that, compared with bisulfite sequencing, TAPS results in higher mapping rates, more even coverage and lower sequencing costs, thus enabling higher quality, more comprehensive and cheaper methylome analyses.
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Affiliation(s)
- Yibin Liu
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paulina Siejka-Zielińska
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gergana Velikova
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ying Bi
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Fang Yuan
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
| | - Marketa Tomkova
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chunsen Bai
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- College of Chemistry, Nankai University, Tianjin, China
| | - Lei Chen
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Center for Mitochondrial Biology and Medicine and Center for Translational Medicine, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Benjamin Schuster-Böckler
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Chun-Xiao Song
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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Yuan F, Bi Y, Siejka-Zielinska P, Zhou YL, Zhang XX, Song CX. Bisulfite-free and base-resolution analysis of 5-methylcytidine and 5-hydroxymethylcytidine in RNA with peroxotungstate. Chem Commun (Camb) 2019; 55:2328-2331. [PMID: 30723849 PMCID: PMC6984333 DOI: 10.1039/c9cc00274j] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 01/30/2019] [Indexed: 01/28/2023]
Abstract
5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), two of the best-studied DNA modifications, play crucial roles in normal development and disease in mammals. Although 5-methylcytidine (m5C) and 5-hydroxymethylcytidine (hm5C) have also been identified in RNA, their distribution and biological function in RNA remain largely unexplored, due to the lack of suitable sequencing methods. Here, we report a base-resolution sequencing method for hm5C in RNA. We applied the selective oxidation of hm5C to trihydroxylated-thymine (thT) mediated by peroxotungstate. thT was subsequently converted to T during cDNA synthesis using a thermostable group II intron reverse transcriptase (TGIRT). Base-resolution analysis of the hm5C sites in RNA was performed using Sanger sequencing. Furthermore, in combination with the TET enzyme oxidation of m5C to hm5C in RNA, we expand the use of peroxotungstate oxidation to detect m5C in RNA at base-resolution. By using this method, we confirmed three known m5C sites in human tRNA, demonstrating the applicability of our method in analyzing real RNA samples.
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Affiliation(s)
- Fang Yuan
- Ludwig Institute for Cancer Research and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK. and Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
| | - Ying Bi
- Ludwig Institute for Cancer Research and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK.
| | - Paulina Siejka-Zielinska
- Ludwig Institute for Cancer Research and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK.
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China.
| | - Chun-Xiao Song
- Ludwig Institute for Cancer Research and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK.
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16
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Parker MJ, Weigele PR, Saleh L. Insights into the Biochemistry, Evolution, and Biotechnological Applications of the Ten-Eleven Translocation (TET) Enzymes. Biochemistry 2019; 58:450-467. [PMID: 30571101 DOI: 10.1021/acs.biochem.8b01185] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A tight link exists between patterns of DNA methylation at carbon 5 of cytosine and differential gene expression in mammalian tissues. Indeed, aberrant DNA methylation results in various human diseases, including neurologic and immune disorders, and contributes to the initiation and progression of various cancers. Proper DNA methylation depends on the fidelity and control of the underlying mechanisms that write, maintain, and erase these epigenetic marks. In this Perspective, we address one of the key players in active demethylation: the ten-eleven translocation enzymes or TETs. These enzymes belong to the Fe2+/α-ketoglutarate-dependent dioxygenase superfamily and iteratively oxidize 5-methylcytosine (5mC) in DNA to produce 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine. The latter three bases may convey additional layers of epigenetic information in addition to being intermediates in active demethylation. Despite the intense interest in understanding the physiological roles TETs play in active demethylation and cell regulation, less has been done, in comparison, to illuminate details of the chemistry and factors involved in regulating the three-step oxidation mechanism. Herein, we focus on what is known about the biochemical features of TETs and explore questions whose answers will lead to a more detailed understanding of the in vivo modus operandi of these enzymes. We also summarize the membership and evolutionary history of the TET/JBP family and highlight the prokaryotic homologues as a reservoir of potentially diverse functionalities awaiting discovery. Finally, we spotlight sequencing methods that utilize TETs for mapping 5mC and its oxidation products in genomic DNA and comment on possible improvements in these approaches.
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Affiliation(s)
- Mackenzie J Parker
- Research Department , New England Biolabs, Inc. , 240 County Road , Ipswich , Massachusetts 01938 , United States
| | - Peter R Weigele
- Research Department , New England Biolabs, Inc. , 240 County Road , Ipswich , Massachusetts 01938 , United States
| | - Lana Saleh
- Research Department , New England Biolabs, Inc. , 240 County Road , Ipswich , Massachusetts 01938 , United States
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17
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Wang Y, Liu C, Wu F, Zhang X, Liu S, Chen Z, Zeng W, Yang W, Zhang X, Zhou Y, Weng X, Wu Z, Zhou X. Highly Selective 5-Formyluracil Labeling and Genome-wide Mapping Using (2-Benzimidazolyl)Acetonitrile Probe. iScience 2018; 9:423-432. [PMID: 30466066 PMCID: PMC6249349 DOI: 10.1016/j.isci.2018.10.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/04/2018] [Accepted: 10/23/2018] [Indexed: 02/08/2023] Open
Abstract
Chemical modifications to nucleobases have a great influence on various cellular processes, by making gene regulation more complex, thus indicating their profound impact on aspects of heredity, growth, and disease. Here, we provide the first genome-wide map of 5-formyluracil (5fU) in living tissues and evaluate the potential roles for 5fU in genomics. We show that an azido derivative of (2-benzimidazolyl)acetonitrile has high selectivity for enriching 5fU-containing genomic DNA. The results have demonstrated the feasibility of using this method to determine the genome-wide distribution of 5fU. Intriguingly, most 5fU sites were found in intergenic regions and introns. Also, distribution of 5fU in human thyroid carcinoma tissues is positively correlated with binding sites of POLR2A protein, which indicates that 5fU may distributed around POLR2A-binding sites. The derivative of (2-benzimidazolyl)acetonitrile (azi-BIAN) can selectivity label 5fU Azi-BIAN can selectively label and pull down 5fU in the genome for NGS The first genome-wide map of 5fU in mammalian genomic DNA 5fU is highly enriched at intergenic regions and introns
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Affiliation(s)
- Yafen Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Chaoxing Liu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Fan Wu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Xiong Zhang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Sheng Liu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, School of Medicine, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Zonggui Chen
- College of Life Science, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Weiwu Zeng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Wei Yang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Xiaolian Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, School of Medicine, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Yu Zhou
- College of Life Science, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Zhiguo Wu
- College of Life Science, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China.
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19
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Kawasaki F, Martínez Cuesta S, Beraldi D, Mahtey A, Hardisty RE, Carrington M, Balasubramanian S. Sequencing 5-Hydroxymethyluracil at Single-Base Resolution. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Fumiko Kawasaki
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Sergio Martínez Cuesta
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
- Cancer Research UK, Cambridge Institute; Li Ka Shing Centre; Robinson Way Cambridge CB2 0RE UK
| | - Dario Beraldi
- Cancer Research UK, Cambridge Institute; Li Ka Shing Centre; Robinson Way Cambridge CB2 0RE UK
| | - Areeb Mahtey
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Robyn E. Hardisty
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Mark Carrington
- Department of Biochemistry; University of Cambridge; Hopkins Building; Tennis Court Road Cambridge CB2 1QW UK
| | - Shankar Balasubramanian
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
- Cancer Research UK, Cambridge Institute; Li Ka Shing Centre; Robinson Way Cambridge CB2 0RE UK
- School of Clinical Medicine; University of Cambridge; Cambridge CB2 0SP UK
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20
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Kawasaki F, Martínez Cuesta S, Beraldi D, Mahtey A, Hardisty RE, Carrington M, Balasubramanian S. Sequencing 5-Hydroxymethyluracil at Single-Base Resolution. Angew Chem Int Ed Engl 2018; 57:9694-9696. [PMID: 29882366 PMCID: PMC6100112 DOI: 10.1002/anie.201804046] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/01/2018] [Indexed: 11/06/2022]
Abstract
5-hydroxymethyluracil (5hmU) is formed through oxidation of thymine both enzymatically and non-enzymatically in various biological systems. Although 5hmU has been reported to affect biological processes such as protein-DNA interactions, the consequences of 5hmU formation in genomes have not been yet fully explored. Herein, we report a method to sequence 5hmU at single-base resolution. We employ chemical oxidation to transform 5hmU to 5-formyluracil (5fU), followed by the polymerase extension to induce T-to-C base changes owing to the inherent ability of 5fU to form 5fU:G base pairing. In combination with the Illumina next generation sequencing technology, we developed polymerase chain reaction (PCR) conditions to amplify the T-to-C base changes and demonstrate the method in three different synthetic oligonucleotide models as well as part of the genome of a 5hmU-rich eukaryotic pathogen. Our method has the potential capability to map 5hmU in genomic DNA and thus will contribute to promote the understanding of this modified base.
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Affiliation(s)
- Fumiko Kawasaki
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Sergio Martínez Cuesta
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Cancer Research UK, Cambridge InstituteLi Ka Shing CentreRobinson WayCambridgeCB2 0REUK
| | - Dario Beraldi
- Cancer Research UK, Cambridge InstituteLi Ka Shing CentreRobinson WayCambridgeCB2 0REUK
| | - Areeb Mahtey
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Robyn E. Hardisty
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Mark Carrington
- Department of BiochemistryUniversity of CambridgeHopkins BuildingTennis Court RoadCambridgeCB2 1QWUK
| | - Shankar Balasubramanian
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Cancer Research UK, Cambridge InstituteLi Ka Shing CentreRobinson WayCambridgeCB2 0REUK
- School of Clinical MedicineUniversity of CambridgeCambridgeCB2 0SPUK
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21
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Ren R, Horton JR, Zhang X, Blumenthal RM, Cheng X. Detecting and interpreting DNA methylation marks. Curr Opin Struct Biol 2018; 53:88-99. [PMID: 30031306 DOI: 10.1016/j.sbi.2018.06.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/19/2018] [Indexed: 12/22/2022]
Abstract
The generation, alteration, recognition, and erasure of epigenetic modifications of DNA are fundamental to controlling gene expression in mammals. These covalent DNA modifications include cytosine methylation by AdoMet-dependent methyltransferases and 5-methylcytosine oxidation by Fe(II)-dependent and α-ketoglutarate-dependent dioxygenases. Sequence-specific transcription factors are responsible for interpreting the modification status of specific regions of chromatin. This review focuses on recent developments in characterizing the functional and structural links between the modification status of two DNA bases: 5-methylcytosine and 5-methyluracil (thymine).
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Affiliation(s)
- Ren Ren
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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22
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23
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Liu C, Zou G, Peng S, Wang Y, Yang W, Wu F, Jiang Z, Zhang X, Zhou X. 5-Formyluracil as a Multifunctional Building Block in Biosensor Designs. Angew Chem Int Ed Engl 2018; 57:9689-9693. [DOI: 10.1002/anie.201804007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/27/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Chaoxing Liu
- College of Chemistry and Molecular Sciences; Key Laboratory of Biomedical Polymers of, Ministry of Education; The Institute for Advanced Studies; Hubei Province Key Laboratory of Allergy and Immunology; Wuhan University; Wuhan Hubei 430072 P. R. China
| | - Guangrong Zou
- College of Chemistry and Molecular Sciences; Key Laboratory of Biomedical Polymers of, Ministry of Education; The Institute for Advanced Studies; Hubei Province Key Laboratory of Allergy and Immunology; Wuhan University; Wuhan Hubei 430072 P. R. China
| | - Shuang Peng
- College of Chemistry and Molecular Sciences; Key Laboratory of Biomedical Polymers of, Ministry of Education; The Institute for Advanced Studies; Hubei Province Key Laboratory of Allergy and Immunology; Wuhan University; Wuhan Hubei 430072 P. R. China
| | - Yafen Wang
- College of Chemistry and Molecular Sciences; Key Laboratory of Biomedical Polymers of, Ministry of Education; The Institute for Advanced Studies; Hubei Province Key Laboratory of Allergy and Immunology; Wuhan University; Wuhan Hubei 430072 P. R. China
| | - Wei Yang
- College of Chemistry and Molecular Sciences; Key Laboratory of Biomedical Polymers of, Ministry of Education; The Institute for Advanced Studies; Hubei Province Key Laboratory of Allergy and Immunology; Wuhan University; Wuhan Hubei 430072 P. R. China
| | - Fan Wu
- College of Chemistry and Molecular Sciences; Key Laboratory of Biomedical Polymers of, Ministry of Education; The Institute for Advanced Studies; Hubei Province Key Laboratory of Allergy and Immunology; Wuhan University; Wuhan Hubei 430072 P. R. China
| | - Zhuoran Jiang
- College of Chemistry and Molecular Sciences; Key Laboratory of Biomedical Polymers of, Ministry of Education; The Institute for Advanced Studies; Hubei Province Key Laboratory of Allergy and Immunology; Wuhan University; Wuhan Hubei 430072 P. R. China
| | - Xiong Zhang
- College of Chemistry and Molecular Sciences; Key Laboratory of Biomedical Polymers of, Ministry of Education; The Institute for Advanced Studies; Hubei Province Key Laboratory of Allergy and Immunology; Wuhan University; Wuhan Hubei 430072 P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences; Key Laboratory of Biomedical Polymers of, Ministry of Education; The Institute for Advanced Studies; Hubei Province Key Laboratory of Allergy and Immunology; Wuhan University; Wuhan Hubei 430072 P. R. China
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24
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Chen Y, Hong T, Wang S, Mo J, Tian T, Zhou X. Epigenetic modification of nucleic acids: from basic studies to medical applications. Chem Soc Rev 2018; 46:2844-2872. [PMID: 28352906 DOI: 10.1039/c6cs00599c] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The epigenetic modification of nucleic acids represents one of the most significant areas of study in the field of nucleic acids because it makes gene regulation more complex and heredity more complicated, thus indicating its profound impact on aspects of heredity, growth, and diseases. The recent characterization of epigenetic modifications of DNA and RNA using chemical labelling strategies has promoted the discovery of these modifications, and the newly developed single-base or single-cell resolution mapping strategies have enabled large-scale epigenetic studies in eukaryotes. Due to these technological breakthroughs, several new epigenetic marks have been discovered that have greatly extended the scope and impact of epigenetic modifications in nucleic acids over the past few years. Because epigenetics is reversible and susceptible to environmental factors, it could potentially be a promising direction for clinical medicine research. In this review, we have comprehensively discussed how these epigenetic marks are involved in disease, including the pathogenesis, prevention, diagnosis and treatment of disease. These findings have revealed that the epigenetic modification of nucleic acids has considerable significance in various areas from methodology to clinical medicine and even in biomedical applications.
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Affiliation(s)
- Yuqi Chen
- College of Chemistry and Molecular Sciences, Institute of Advanced Studies, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Hubei, Wuhan 430072, P. R. China.
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25
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26
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Carell T, Kurz MQ, Müller M, Rossa M, Spada F. Non-canonical Bases in the Genome: The Regulatory Information Layer in DNA. Angew Chem Int Ed Engl 2018; 57:4296-4312. [DOI: 10.1002/anie.201708228] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Thomas Carell
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
| | - Matthias Q. Kurz
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
| | - Markus Müller
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
| | - Martin Rossa
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
| | - Fabio Spada
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
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27
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Hardwick JS, Lane AN, Brown T. Epigenetic Modifications of Cytosine: Biophysical Properties, Regulation, and Function in Mammalian DNA. Bioessays 2018; 40. [DOI: 10.1002/bies.201700199] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/13/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Jack S. Hardwick
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Andrew N. Lane
- Department of Toxicology and Cancer Biology; University of Kentucky; 789 S. Limestone St. Lexington KY 40536 USA
| | - Tom Brown
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
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28
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Raiber EA, Hardisty R, van Delft P, Balasubramanian S. Mapping and elucidating the function of modified bases in DNA. Nat Rev Chem 2017. [DOI: 10.1038/s41570-017-0069] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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29
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Bullard W, Kieft R, Sabatini R. A method for the efficient and selective identification of 5-hydroxymethyluracil in genomic DNA. Biol Methods Protoc 2017; 2. [PMID: 29276783 PMCID: PMC5741180 DOI: 10.1093/biomethods/bpw006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Recently, 5-hydroxymethyluracil (5hmU) was identified in mammalian genomic DNA as an oxidative product of thymine by the ten-eleven translocation (TET) proteins. While the biological role of this modification remains unclear, identifying its genomic location will assist in elucidating function. Here we present a rapid and robust method to selectively tag and enrich genomic regions containing 5hmU. This method involves the selective glucosylation of 5hmU residues by the base J glucosyltransferase from trypanosomes creating glucosylhydroxymethyluracil (base J). The base J can then be efficiently and selectively pulled down by antibodies against base J or by J-binding protein 1. DNA that is enriched is suitable for analysis by quantitative PCR or sequencing. We utilized this tagging reaction to provide proof of concept for the enrichment of 5hmU containing DNA from a pool that contains modified and unmodified DNA. Furthermore, we demonstrate that the base J pull-down assay identifies 5hmU at specific regions of the trypanosome genome involved in transcriptional repression. The method described here will allow for a greater understanding of the functional role and dynamics of 5hmU in biology.
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Affiliation(s)
- Whitney Bullard
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Rudo Kieft
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Robert Sabatini
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
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Kawasaki F, Murat P, Li Z, Santner T, Balasubramanian S. Synthesis and biophysical analysis of modified thymine-containing DNA oligonucleotides. Chem Commun (Camb) 2017; 53:1389-1392. [PMID: 28074944 PMCID: PMC5759927 DOI: 10.1039/c6cc08670e] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report the synthesis of a 5-formyl-2'-deoxyuridine (5fU) phosphoramidite and the preparation of oligonucleotides comprising all known, naturally observed eukaryotic thymidine modifications. Biophysical characterization of the synthetic oligonucleotides indicates that 5fU, but not the other T-derivatives, can alter DNA structures.
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Affiliation(s)
- F Kawasaki
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - P Murat
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Z Li
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - T Santner
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - S Balasubramanian
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK and School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SP, UK
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31
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Bochtler M, Kolano A, Xu GL. DNA demethylation pathways: Additional players and regulators. Bioessays 2016; 39:1-13. [PMID: 27859411 DOI: 10.1002/bies.201600178] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DNA demethylation can occur passively by "dilution" of methylation marks by DNA replication, or actively and independently of DNA replication. Direct conversion of 5-methylcytosine (5mC) to cytosine (C), as originally proposed, does not occur. Instead, active DNA methylation involves oxidation of the methylated base by ten-eleven translocations (TETs), or deamination of the methylated or a nearby base by activation induced deaminase (AID). The modified nucleotide, possibly together with surrounding nucleotides, is then replaced by the BER pathway. Recent data clarify the roles and the regulation of well-known enzymes in this process. They identify base excision repair (BER) glycosylases that may cooperate with or replace thymine DNA glycosylase (TDG) in the base excision step, and suggest possible involvement of DNA damage repair pathways other than BER in active DNA demethylation. Here, we review these new developments.
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Affiliation(s)
- Matthias Bochtler
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Kolano
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Guo-Liang Xu
- Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
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Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM, Zhang X, Cheng X. Distinctive Klf4 mutants determine preference for DNA methylation status. Nucleic Acids Res 2016; 44:10177-10185. [PMID: 27596594 PMCID: PMC5137437 DOI: 10.1093/nar/gkw774] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 01/06/2023] Open
Abstract
Reprogramming of mammalian genome methylation is critically important but poorly understood. Klf4, a transcription factor directing reprogramming, contains a DNA binding domain with three consecutive C2H2 zinc fingers. Klf4 recognizes CpG or TpG within a specific sequence. Mouse Klf4 DNA binding domain has roughly equal affinity for methylated CpG or TpG, and slightly lower affinity for unmodified CpG. The structural basis for this key preference is unclear, though the side chain of Glu446 is known to contact the methyl group of 5-methylcytosine (5mC) or thymine (5-methyluracil). We examined the role of Glu446 by mutagenesis. Substituting Glu446 with aspartate (E446D) resulted in preference for unmodified cytosine, due to decreased affinity for 5mC. In contrast, substituting Glu446 with proline (E446P) increased affinity for 5mC by two orders of magnitude. Structural analysis revealed hydrophobic interaction between the proline's aliphatic cyclic structure and the 5-methyl group of the pyrimidine (5mC or T). As in wild-type Klf4 (E446), the proline at position 446 does not interact directly with either the 5mC N4 nitrogen or the thymine O4 oxygen. In contrast, the unmethylated cytosine's exocyclic N4 amino group (NH2) and its ring carbon C5 atom hydrogen bond directly with the aspartate carboxylate of the E446D variant. Both of these interactions would provide a preference for cytosine over thymine, and the latter one could explain the E446D preference for unmethylated cytosine. Finally, we evaluated the ability of these Klf4 mutants to regulate transcription of methylated and unmethylated promoters in a luciferase reporter assay.
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Affiliation(s)
| | - Dongxue Wang
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Alyse N Steves
- Genetics and Molecular Biology Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology & Immunology and Program in Bioinformatics, The University of Toledo College of Medicine & Life Sciences, Toledo, Ohio 43614, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA .,Genetics and Molecular Biology Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30322, USA
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Abstract
In eukaryotic DNA, cytosine can be enzymatically modified to yield up to four epigenetic base variants. DNA methyltransferases convert cytosine to 5-methylcytosine (mC), which plays critical roles in gene regulation during development. Ten-eleven translocation (TET) enzymes can sequentially oxidize mC to three products: 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxylcytosine (caC). These oxidized bases have been found in numerous mammalian cell types, where they potentially carry out independent epigenetic functions and aid in DNA demethylation. To gain insight into the mechanisms and functions of TET family enzymes, rigorous approaches are needed to quantify genomic cytosine modifications in cells and track TET enzyme activity in vitro. Here, we present tools developed by our lab and others to report on each of the five forms of cytosine (unmodified, mC, hmC, fC, and caC) with high specificity and sensitivity. We provide detailed protocols for qualitative and quantitative analysis of cytosine modifications in genomic DNA by dot blotting and LC-MS/MS. We then describe methods for generating synthetic oligonucleotide substrates for biochemical studies, provide optimized reaction conditions, and introduce several chemoenzymatic assays, as well as HPLC, mass spectrometry, and scintillation counting methods to quantify cytosine modifications in vitro. These approaches enable mechanistic studies of TET activity, which are key to understanding the role of these enzymes in epigenetic regulation.
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Olinski R, Starczak M, Gackowski D. Enigmatic 5-hydroxymethyluracil: Oxidatively modified base, epigenetic mark or both? MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2016; 767:59-66. [DOI: 10.1016/j.mrrev.2016.02.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/05/2016] [Accepted: 02/07/2016] [Indexed: 11/24/2022]
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Hong S, Cheng X. DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:321-341. [PMID: 27826845 DOI: 10.1007/978-3-319-43624-1_14] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The modification of DNA bases is a classic hallmark of epigenetics. Four forms of modified cytosine-5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine-have been discovered in eukaryotic DNA. In addition to cytosine carbon-5 modifications, cytosine and adenine methylated in the exocyclic amine-N4-methylcytosine and N6-methyladenine-are other modified DNA bases discovered even earlier. Each modified base can be considered a distinct epigenetic signal with broader biological implications beyond simple chemical changes. Since 1994, crystal structures of proteins and enzymes involved in writing, reading, and erasing modified bases have become available. Here, we present a structural synopsis of writers, readers, and erasers of the modified bases from prokaryotes and eukaryotes. Despite significant differences in structures and functions, they are remarkably similar regarding their engagement in flipping a target base/nucleotide within DNA for specific recognitions and/or reactions. We thus highlight base flipping as a common structural framework broadly applied by distinct classes of proteins and enzymes across phyla for epigenetic regulations of DNA.
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Affiliation(s)
- Samuel Hong
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA, 30322, USA. .,Molecular and Systems Pharmacology Graduate Program, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA, 30322, USA.
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA, 30322, USA
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36
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Iyer LM, Zhang D, Aravind L. Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification. Bioessays 2015; 38:27-40. [PMID: 26660621 PMCID: PMC4738411 DOI: 10.1002/bies.201500104] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
While N6‐methyladenosine (m6A) is a well‐known epigenetic modification in bacterial DNA, it remained largely unstudied in eukaryotes. Recent studies have brought to fore its potential epigenetic role across diverse eukaryotes with biological consequences, which are distinct and possibly even opposite to the well‐studied 5‐methylcytosine mark. Adenine methyltransferases appear to have been independently acquired by eukaryotes on at least 13 occasions from prokaryotic restriction‐modification and counter‐restriction systems. On at least four to five instances, these methyltransferases were recruited as RNA methylases. Thus, m6A marks in eukaryotic DNA and RNA might be more widespread and diversified than previously believed. Several m6A‐binding protein domains from prokaryotes were also acquired by eukaryotes, facilitating prediction of potential readers for these marks. Further, multiple lineages of the AlkB family of dioxygenases have been recruited as m6A demethylases. Although members of the TET/JBP family of dioxygenases have also been suggested to be m6A demethylases, this proposal needs more careful evaluation. Also watch the Video Abstract.
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Affiliation(s)
- Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Dapeng Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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37
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Hashimoto H, Pais JE, Dai N, Corrêa IR, Zhang X, Zheng Y, Cheng X. Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA. Nucleic Acids Res 2015; 43:10713-21. [PMID: 26323320 PMCID: PMC4678852 DOI: 10.1093/nar/gkv870] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/19/2015] [Indexed: 01/15/2023] Open
Abstract
The family of ten-eleven translocation (Tet) dioxygenases is widely distributed across the eukaryotic tree of life, from mammals to the amoeboflagellate Naegleria gruberi. Like mammalian Tet proteins, the Naegleria Tet-like protein, NgTet1, acts on 5-methylcytosine (5mC) and generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) in three consecutive, Fe(II)- and α-ketoglutarate-dependent oxidation reactions. The two intermediates, 5hmC and 5fC, could be considered either as the reaction product of the previous enzymatic cycle or the substrate for the next cycle. Here we present a new crystal structure of NgTet1 in complex with DNA containing a 5hmC. Along with the previously solved NgTet1–5mC structure, the two complexes offer a detailed picture of the active site at individual stages of the reaction cycle. In the crystal, the hydroxymethyl (OH-CH2-) moiety of 5hmC points to the metal center, representing the reaction product of 5mC hydroxylation. The hydroxyl oxygen atom could be rotated away from the metal center, to a hydrophobic pocket formed by Ala212, Val293 and Phe295. Such rotation turns the hydroxyl oxygen atom away from the product conformation, and exposes the target CH2 towards the metal-ligand water molecule, where a dioxygen O2 molecule would occupy to initiate the next round of reaction by abstracting a hydrogen atom from the substrate. The Ala212-to-Val (A212V) mutant profoundly limits the product to 5hmC, probably because the reduced hydrophobic pocket size restricts the binding of 5hmC as a substrate.
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Affiliation(s)
- Hideharu Hashimoto
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - June E Pais
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Nan Dai
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Ivan R Corrêa
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - Yu Zheng
- RGENE Inc., 953 Indiana Street, San Francisco, CA, 94107, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
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38
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Hashimoto H, Zhang X, Vertino PM, Cheng X. The Mechanisms of Generation, Recognition, and Erasure of DNA 5-Methylcytosine and Thymine Oxidations. J Biol Chem 2015; 290:20723-20733. [PMID: 26152719 DOI: 10.1074/jbc.r115.656884] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
One of the most fundamental questions in the control of gene expression in mammals is how the patterns of epigenetic modifications of DNA are generated, recognized, and erased. This includes covalent cytosine methylation of DNA and its associated oxidation states. An array of AdoMet-dependent methyltransferases, Fe(II)- and α-ketoglutarate-dependent dioxygenases, base excision glycosylases, and sequence-specific transcription factors is responsible for changing, maintaining, and interpreting the modification status of specific regions of chromatin. This review focuses on recent developments in characterizing the functional and structural links between the modification status of two DNA bases 5-methylcytosine and thymine (5-methyluracil).
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Affiliation(s)
- Hideharu Hashimoto
- Departments of Biochemistry, Emory University School of Medicine, Emory University, Atlanta, Georgia 30322
| | - Xing Zhang
- Departments of Biochemistry, Emory University School of Medicine, Emory University, Atlanta, Georgia 30322
| | - Paula M Vertino
- Departments of Radiation Oncology, Emory University School of Medicine, Emory University, Atlanta, Georgia 30322; Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
| | - Xiaodong Cheng
- Departments of Biochemistry, Emory University School of Medicine, Emory University, Atlanta, Georgia 30322; Winship Cancer Institute, Emory University, Atlanta, Georgia 30322.
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