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Yoshimura A, Saeki R, Nakada R, Tomimoto S, Jomori T, Suganuma K, Wakimoto T. Membrane-Vesicle-Mediated Interbacterial Communication Activates Silent Secondary Metabolite Production. Angew Chem Int Ed Engl 2023; 62:e202307304. [PMID: 37449463 DOI: 10.1002/anie.202307304] [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: 05/24/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Most bacterial biosynthetic gene clusters (BGCs) are "silent BGCs" that are expressed poorly or not at all under normal culture conditions. However, silent BGCs, even in part, may be conditionally expressed in response to external stimuli in the original bacterial habitats. The growing knowledge of bacterial membrane vesicles (MVs) suggests that they could be promising imitators of the exogenous stimulants, especially given their functions as signaling mediators in bacterial cell-to-cell communication. Therefore, we envisioned that MVs added to bacterial cultures could activate diverse silent BGCs. Herein, we employed Burkholderia multivorans MVs, which induced silent metabolites in a wide range of bacteria in Actinobacteria, Bacteroidetes and Proteobacteria phyla. A mechanistic analysis of MV-induced metabolite production in Xenorhabdus innexi suggested that the B. multivorans MVs activate silent metabolite production by inhibiting quorum sensing in X. innexi. In turn, the X. innexi MVs carrying some MV-induced peptides suppressed the growth of B. multivorans, highlighting the interspecies communication between B. multivorans and X. innexi through MV exchange.
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Affiliation(s)
- Aya Yoshimura
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Rio Saeki
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Ryusuke Nakada
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Shota Tomimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Takahiro Jomori
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
- Faculty of Science, University of the Ryukyus, 1-Senbaru, Nishihara, Nakagami, Okinawa, 903-0213, Japan
| | - Keisuke Suganuma
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, 080-8555, Japan
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine Inada, Obihiro, 080-8555, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
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2
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Hawass MAE, Sanad SMH, Elwahy AHM, Abdelhamid IA. Hantzsch synthesis of bis(pyrido[2,3-d:6,5-d']dipyrimidines), bis(pyrimido[4,5-b]quinolines), and bis(benzo[4,5]imidazo[2,1-b]quinazolines) linked to pyrazole units as novel hybrid molecules. SYNTHETIC COMMUN 2021. [DOI: 10.1080/00397911.2021.1913604] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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3
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Abe M, Kagara N, Miyake T, Tanei T, Naoi Y, Shimoda M, Shimazu K, Kim SJ, Noguchi S. Highly sensitive detection of sentinel lymph node metastasis of breast cancer by digital PCR for RASSF1A methylation. Oncol Rep 2019; 42:2382-2389. [PMID: 31638213 PMCID: PMC6826319 DOI: 10.3892/or.2019.7363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/19/2019] [Indexed: 12/19/2022] Open
Abstract
One-step nucleic acid amplification (OSNA) targeting cytokeratin 19 (CK19) mRNA expression and pathological examination are widely used for the intraoperative diagnosis of sentinel node (SN) metastasis. The aim of the present study was to develop a novel assay for detecting SN metastasis by targeting Ras association domain-containing protein 1 (RASSF1A) methylation in tumor cells, and to compare its performance with OSNA. Using digital PCR with methylation-specific restriction enzymes (RE-dMSP), our assay was able to detect ≥3 copies of methylated DNA per well, and was ≥10 times more sensitive than real-time PCR with bisulfite modification. OSNA lysates were examined using RE-dMSP and digital PCR for PIK3CA mutation, in the event that primary tumors were PIK3CA mutation-positive. RE-dMSP revealed a high concordance of 95.0% (153/161) with OSNA, and 100% (59/59) with PIK3CA mutation for detecting SN metastasis. In 11 breast cancer cell lines, the variation in methylated RASSF1A copy number was significantly lower than that of CK19 mRNA (2.8 vs. 10.5-fold; P<0.01). RE-dMSP has the potential to more accurately detect SN metastasis, and to more precisely estimate total tumor loads in SN, compared with OSNA.
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Affiliation(s)
- Mizuho Abe
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565‑0871, Japan
| | - Naofumi Kagara
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565‑0871, Japan
| | - Tomohiro Miyake
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565‑0871, Japan
| | - Tomonori Tanei
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565‑0871, Japan
| | - Yasuto Naoi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565‑0871, Japan
| | - Masafumi Shimoda
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565‑0871, Japan
| | - Kenzo Shimazu
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565‑0871, Japan
| | - Seung Jin Kim
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565‑0871, Japan
| | - Shinzaburo Noguchi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565‑0871, Japan
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4
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Tarn BE, Sung KJ, Sikes HD. Engineering affinity agents for the detection of hemi-methylated CpG sites in DNA. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2016; 1:273-277. [PMID: 28580176 PMCID: PMC5450655 DOI: 10.1039/c6me00073h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Wild-type methyl-CpG-binding domain (MBD) proteins specifically bind symmetrically methylated DNA sequences, and assays have been developed that use these proteins for profiling DNA methylation. Here, we use directed evolution in the yeast surface display format to identify a new protein variant that binds hemi-methylated CpG dinucleotides.
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Affiliation(s)
- B E Tarn
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - K-J Sung
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - H D Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
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5
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Heimer BW, Tam BE, Minkovsky A, Sikes HD. Using nanobiotechnology to increase the prevalence of epigenotyping assays in precision medicine. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2016; 9. [PMID: 27126368 DOI: 10.1002/wnan.1407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/07/2016] [Accepted: 03/17/2016] [Indexed: 12/31/2022]
Abstract
Epigenetic silencing of genes that are important for DNA repair, cell cycle control, apoptosis, and cellular interactions with the extracellular matrix has been causally linked to several subtypes of cancer. Translating this knowledge of the implications of promoter methylation to wide and routine use in clinical pathology laboratories has been more challenging than the case of genetic analyses because epigenetic modifications do not change the underlying sequence of the affected nucleic acid, rendering polymerase chain reaction analysis alone uninformative. Two epigenotyping assays that detect promoter methylation are currently standard of care in treatment of two distinct tumor types in only a few top hospitals across the United States. Both rely on a harsh chemical step that degrades over 90% of tumor DNA samples, which are often available in limited quantities, and imparts the potential for false-negative or false-positive results if the reaction conditions are not exactly correct. Using nanotechnology and biotechnology to devise practical new analysis techniques that avoid the drawbacks of current techniques represents a powerful approach that is likely to significantly increase the clinical use of this class of biomarkers in the coming years. WIREs Nanomed Nanobiotechnol 2017, 9:e1407. doi: 10.1002/wnan.1407 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Brandon W Heimer
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brooke E Tam
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alissa Minkovsky
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Hadley D Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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6
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Okamoto A. Nucleic Acid Reaction Chemistry to Clarify the Fluctuating Quality and Quantity of Nucleic Acids. J SYN ORG CHEM JPN 2016. [DOI: 10.5059/yukigoseikyokaishi.74.474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Akimitsu Okamoto
- Research Center for Advanced Science and Technology, The University of Tokyo
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7
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Gao C, Li H, Liu Y, Wei W, Zhang Y, Liu S. Label-free fluorescence detection of DNA methylation and methyltransferase activity based on restriction endonuclease HpaII and exonuclease III. Analyst 2014; 139:6387-92. [DOI: 10.1039/c4an01359j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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8
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Okamoto A. DNA-Osmium Complexes: Recent Developments in the Operative Chemical Analysis of DNA Epigenetic Modifications. ChemMedChem 2014; 9:1958-65. [DOI: 10.1002/cmdc.201402114] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Indexed: 12/26/2022]
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9
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Sarmah MM, Prajapati D. Exploration of uracils: pot and step economic production of pyridine core containing templates by multicomponent aza-Diels–Alder reaction. RSC Adv 2014. [DOI: 10.1039/c4ra02273d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Substituted pyrido[2,3-d]pyrimidines can be obtained with good yields via a multicomponent aza-Diels–Alder reaction from easily available starting materials. The diene behaviour of different uracil derivatives was also elaborately investigated to synthesize desired products.
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Affiliation(s)
- Manas M. Sarmah
- Medicinal Chemistry Division
- CSIR-North-East Institute of Science and Technology
- Jorhat, India
| | - Dipak Prajapati
- Medicinal Chemistry Division
- CSIR-North-East Institute of Science and Technology
- Jorhat, India
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10
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Nanorod-Shaped Basic Al2O3 Catalyzed N,N-Diformylation of Bisuracil Derivatives: A Greener "NOSE" Approach. ISRN ORGANIC CHEMISTRY 2013; 2013:793159. [PMID: 24052870 PMCID: PMC3767338 DOI: 10.1155/2013/793159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 06/10/2013] [Indexed: 12/04/2022]
Abstract
A feasible “NOSE” (nanoparticles-catalyzed organic synthesis enhancement) protocol has been developed for N,N-diformylation of bisuracil derivatives using nano-Al2O3 rods as an efficient, inexpensive, and recyclable catalyst under solvent-free reaction condition at 40°C. The catalyst was reused up to the 4th cycle without affecting the rate and yield of the N,N-diformylation products appreciably.
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11
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Hu J, Xing X, Xu X, Wu F, Guo P, Yan S, Xu Z, Xu J, Weng X, Zhou X. Selective chemical labelling of 5-formylcytosine in DNA by fluorescent dyes. Chemistry 2013; 19:5836-40. [PMID: 23512548 DOI: 10.1002/chem.201300082] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Indexed: 12/27/2022]
Abstract
Direct labelling: 5-Formylcytosine in DNA can be selectively labelled by fluorescent dyes containing an active amino group. The labelled DNA shows strong fluorescence and can be detected by polyacrylamide gel electrophoresis (PAGE) and fluorescence measurements (see scheme). This method can distinguish 5-formylcytosine from other methylation forms of cytosine in DNA.
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Affiliation(s)
- Jianlin Hu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, PR China
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12
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Fujimo K, Konishi-Hiratsuka K, Sakamoto T. Quick, Selective and Reversible Photocrosslinking Reaction between 5-Methylcytosine and 3-Cyanovinylcarbazole in DNA Double Strand. Int J Mol Sci 2013; 14:5765-74. [PMID: 23481638 PMCID: PMC3634424 DOI: 10.3390/ijms14035765] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/12/2013] [Accepted: 02/26/2013] [Indexed: 02/02/2023] Open
Abstract
Selective photocrosslinking reaction between 3-cyanovinylcarbazole nucleoside (CNVK) and 5-methylcytosine (mC), which is known as epigenetic modification in genomic DNA, was developed. The reaction was completely finished within 5 s of 366 nm irradiation, and the rate of this photocrosslinking reaction was ca. 30-fold higher than that in the case of unmodified normal cytosine. There were no significant differences in the thermodynamic parameters and the kinetics of hybrid formation of oligonucleotide (ODN) containing CNVK and its complementary ODN containing C or mC at the photocrosslinking site, and suggesting that the quick and selective photoreaction has potential for the selective detection of mC in the DNA strand via the photocrosslinking reaction.
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Affiliation(s)
- Kenzo Fujimo
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan; E-Mails: (K.K.-H.); (T.S.)
- Research Center for Bio-Architecture, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
- Author to whom correspondence should be addressed; E-Mail: ; Tel./Fax: +81-761-51-1671
| | - Kaoru Konishi-Hiratsuka
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan; E-Mails: (K.K.-H.); (T.S.)
| | - Takashi Sakamoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan; E-Mails: (K.K.-H.); (T.S.)
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13
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Ligand-Incorporation Site in 5-Methylcytosine-Detection Probe Modulating the Site of Osmium Complexation with the Target DNA. Chem Biodivers 2012; 9:2000-7. [DOI: 10.1002/cbdv.201100425] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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14
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Tainaka K, Okamoto A. ICON probes: synthesis and DNA methylation typing. ACTA ACUST UNITED AC 2012; Chapter 8:Unit 8.7.1-17. [PMID: 22147422 DOI: 10.1002/0471142700.nc0807s47] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
DNA methylation and demethylation significantly affect the deactivation and activation processes of gene expression, respectively. The determination of the location and frequency of DNA methylation is important for the elucidation of the mechanisms of cell differentiation and carcinogenesis and may be a useful and effective index for cancer diagnosis. We have developed an artificial DNA probe that induces a methylation detection reaction of a target cytosine in a long DNA sequence (ICON probe). This artificial DNA allows the rapid detection of a methyl group attached at the C5 position of the target cytosine. In addition, there is no nonspecific cleavage of genomic DNA in this reaction. The ICON probe also facilitates the quantification of methylation at the target cytosine using a small amount of genomic DNA sample. This unit provides a procedure for synthesizing bipyridine-modified adenosine phosphoramidite and preparation of ICON probes. Additionally, the protocol for the methylation quantification experiments by quantitative PCR utilizing ICON probes is also presented.
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Affiliation(s)
- Kazuki Tainaka
- Advanced Science Institute, RIKEN, The Institute of Physical and Chemical Research, Wako, Saitama, Japan
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15
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Kawai K, Hayashi M, Majima T. HOMO energy gap dependence of hole-transfer kinetics in DNA. J Am Chem Soc 2012; 134:4806-11. [PMID: 22335550 DOI: 10.1021/ja2109213] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
DNA consists of two type of base-pairs, G-C and A-T, in which the highest occupied molecular orbital (HOMO) localizes on the purine bases G and A. While the hole transfer through consecutive Gs or As occurs faster than 10(9) s(-1), a significant drop in the hole transfer rate was observed for G-C and A-T mixed random sequences. In this study, by using various natural and artificial nucleobases having different HOMO levels, the effect of the HOMO-energy gap between bases (Δ(HOMO)) on the hole-transfer kinetics in DNA was investigated. The results demonstrated that the hole transfer rate can be increased by decreasing the Δ(HOMO) and can be finely tuned over 3 orders of magnitude by varying the Δ(HOMO).
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Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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16
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Sakamoto T, Ami T, Fujimoto K. 5-Methylcytosine Selective Photoligation Using Photoresponsive Oligonucleotides Containing Various 5-Vinyl-2′-deoxyuridines Having an Aromatic Group. CHEM LETT 2012. [DOI: 10.1246/cl.2012.47] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Takashi Sakamoto
- School of Materials Science, Japan Advanced Institute of Science and Technology
| | - Takehiro Ami
- School of Materials Science, Japan Advanced Institute of Science and Technology
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology
- Research Center for Bio-Architecture, Japan Advanced Institute of Science and Technology
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18
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Dohno C, Shibata T, Nakatani K. Interstrand Crosslink for Discrimination of Methylated Cytosines. CHEM LETT 2011. [DOI: 10.1246/cl.2011.852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Abstract
Research in nucleic acids has made major advances in the past decade in multiple fields of science and technology. Here we discuss some of the most important findings in DNA and RNA research in the fields of biology, chemistry, biotechnology, synthetic biology, nanostructures and optical materials, with emphasis on how chemistry has impacted, and is impacted by, these developments. Major challenges ahead include the development of new chemical strategies that allow synthetically modified nucleic acids to enter into, and function in, living systems.
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Affiliation(s)
- Omid Khakshoor
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA. Fax: +1 650 725 0259; Tel: +1 650 724 4741
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA. Fax: +1 650 725 0259; Tel: +1 650 724 4741
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20
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Nomura A, Sugizaki K, Yanagisawa H, Okamoto A. Discrimination between 5-hydroxymethylcytosine and 5-methylcytosine by a chemically designed peptide. Chem Commun (Camb) 2011; 47:8277-9. [PMID: 21695309 DOI: 10.1039/c1cc12131f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
An artificial phosphopeptide recognized the difference between methylated and hydroxymethylated cytosines in DNA. The Sp1 zinc finger peptide substituted by phosphotyrosine effectively discriminated between 5-methylcytosine, 5-hydroxymethylcytosine ((hm)C) and unmethylated cytosine. The DNA recognition properties of the peptide differ from those of other chemicals that detect (hm)C.
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Affiliation(s)
- Akiko Nomura
- Advanced Science Institute, RIKEN, Wako, Saitama 351-0198, Japan
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21
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Münzel M, Globisch D, Carell T. 5-Hydroxymethylcytosine, the sixth base of the genome. Angew Chem Int Ed Engl 2011; 50:6460-8. [PMID: 21688365 DOI: 10.1002/anie.201101547] [Citation(s) in RCA: 187] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Indexed: 01/17/2023]
Abstract
5-Hydroxymethylcytosine (hmC) was recently discovered as a new constituent of mammalian DNA. Besides 5-methylcytosine (mC), it is the only other modified base in higher organisms. The discovery is of enormous importance because it shows that the methylation of cytosines to imprint epigenetic information is not a final chemical step that leads to gene silencing but that further chemistry occurs at the methyl group that might have regulatory function. Recent progress in hmC detection--most notably LC-MS and glucosyltransferase assays--helped to decipher the precise distribution of hmC in the body. This led to the surprising finding that, in contrast to constant mC levels, the hmC levels are strongly tissue-specific. The highest values of hmC are found in the central nervous system. It was furthermore discovered that hmC is involved in regulating the pluripotency of stem cells and that it is connected to the processes of cellular development and carcinogenesis. Evidence is currently accumulating that hmC may not exclusively be an intermediate of an active demethylation process, but that it functions instead as an important epigenetic marker.
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Affiliation(s)
- Martin Münzel
- Center for Integrated Protein Science, Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377 Munich, Germany
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22
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Münzel M, Globisch D, Carell T. 5-Hydroxymethylcytosin, die sechste Base des Genoms. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101547] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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23
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Hocek M, Fojta M. Nucleobase modification as redox DNA labelling for electrochemical detection. Chem Soc Rev 2011; 40:5802-14. [PMID: 21625726 DOI: 10.1039/c1cs15049a] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Basic aspects of DNA electrochemistry with a strong focus on the use of modified nucleobases as redox probes for electrochemical bioanalysis are reviewed. Intrinsic electrochemical properties of nucleobases in combination with artificial redox-active nucleobase modifications are frequently applied in this field. Synthetic approaches (both chemical and enzymatic) to base-modified nucleic acids are briefly summarized and their applications in redox labelling are discussed. Finally, analytical applications including DNA hybridization, primer extension, PCR, SNP typing, DNA damage and DNA-protein interaction analysis are presented (critical review, 91 references).
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Prague, Czech Republic.
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Sugizaki K, Umemoto T, Okamoto A. On-chip DNA methylation analysis using osmium complexation. J Nucleic Acids 2011; 2011:480570. [PMID: 21772994 PMCID: PMC3136155 DOI: 10.4061/2011/480570] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 04/01/2011] [Indexed: 11/20/2022] Open
Abstract
The development of a reaction for detecting the presence/absence of one methyl group in a long DNA strand is a chemically and biologically challenging research subject. A newly designed chemical assay on a chip for the typing of DNA methylation has been developed. A methylation-detection probe fixed at the bottom of microwells was crosslinked with methylated DNA mediated by osmium complexation and contributes to selective amplification of methylated DNA.
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Affiliation(s)
- Kaori Sugizaki
- Nucleic Acid Chemistry Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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25
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Lewandowska J, Bartoszek A. DNA methylation in cancer development, diagnosis and therapy--multiple opportunities for genotoxic agents to act as methylome disruptors or remediators. Mutagenesis 2011; 26:475-87. [PMID: 21551264 DOI: 10.1093/mutage/ger019] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The role of DNA methylation and recently discovered hydroxymethylation in the function of the human epigenome is currently one of the hottest topics in the life sciences. Progress in this field of research has been further accelerated by the discovery that alterations in the methylome are not only associated with key functions of cells and organisms, such as development, differentiation and gene expression, but may underlie a number of human diseases, including cancer. This review describes both well established and more recent observations concerning alterations in the methylome, i.e. the global and local distribution of 5-methylcytosines, involved in its normal functions. Then, the changes in DNA methylation pattern seen in cancer cells are discussed in the context of their utilisation in cancer diagnostics and treatment. On this basis, comparisons are made between natural covalent DNA modification and that induced by genotoxic agents, chemical carcinogens and antitumour drugs as regards their impact on epigenetic mechanisms. The available data suggest that DNA damage by genotoxins can mimic epigenetic markers and in consequence disrupt the proper function of the epigenome. On the other hand, the same processes in cancer cells, e.g. DNA demethylation as a result of DNA methyltransferase blocking or the induction of DNA repair by DNA adducts, may restore the activity of hypermethylated anticancer genes. The observed multiple mechanisms by which genotoxic agents directly affect methylome function suggest that chemical carcinogens act primarily as epigenome disruptors, whereas mutations are secondary events that occur at later stages of cancer development when genome-protecting mechanisms have already been deregulated.
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Affiliation(s)
- Joanna Lewandowska
- Chemical Faculty, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
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Sugizaki K, Ikeda S, Yanagisawa H, Okamoto A. Facile synthesis of hydroxymethylcytosine-containing oligonucleotides and their reactivity upon osmium oxidation. Org Biomol Chem 2011; 9:4176-81. [PMID: 21499601 DOI: 10.1039/c1ob05247k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA strands containing a 5-hydroxymethylcytosine ((hm)C), which have recently been found in neuron cells and embryonic stem cells, were synthesized through a facile synthetic technique. The (hm)C-containing strands were efficiently oxidized at (hm)C using an osmium oxidation assay. The (hm)C was oxidized as easily as 5-methylcytosine, which can be distinguished from unmethylated cytosine.
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Affiliation(s)
- Kaori Sugizaki
- Advanced Science Institute, RIKEN, Wako, Saitama 351-0198, Japan
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Behm-Ansmant I, Helm M, Motorin Y. Use of specific chemical reagents for detection of modified nucleotides in RNA. J Nucleic Acids 2011; 2011:408053. [PMID: 21716696 PMCID: PMC3118635 DOI: 10.4061/2011/408053] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 01/24/2011] [Indexed: 12/18/2022] Open
Abstract
Naturally occurring cellular RNAs contain an impressive number of chemically distinct modified residues which appear posttranscriptionally, as a result of specific action of the corresponding RNA modification enzymes. Over 100 different chemical modifications have been identified and characterized up to now. Identification of the chemical nature and exact position of these modifications is typically based on 2D-TLC analysis of nucleotide digests, on HPLC coupled with mass spectrometry, or on the use of primer extension by reverse transcriptase. However, many modified nucleotides are silent in reverse transcription, since the presence of additional chemical groups frequently does not change base-pairing properties. In this paper, we give a summary of various chemical approaches exploiting the specific reactivity of modified nucleotides in RNA for their detection.
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Affiliation(s)
- Isabelle Behm-Ansmant
- Laboratoire ARN-RNP Maturation-Structure-Fonction, Enzymologie Moléculaire et Structurale (AREMS), UMR 7214 CNRS-UHP, Nancy Université, boulevard des Aiguillettes, BP 70239, 54506 Vandoeuvre-les-Nancy, France
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Nomura A, Okamoto A. Phosphopeptides Designed for 5-Methylcytosine Recognition. Biochemistry 2011; 50:3376-85. [DOI: 10.1021/bi102053d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Akiko Nomura
- Advanced Science Institute, RIKEN, Wako, Saitama 351-0198, Japan
| | - Akimitsu Okamoto
- Advanced Science Institute, RIKEN, Wako, Saitama 351-0198, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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Das S, Thakur AJ. A Clean, Highly Efficient and One-Pot Green Synthesis of Aryl/Alkyl/Heteroaryl-Substituted Bis(6-amino-1,3-dimethyluracil-5-yl)methanes in Water. European J Org Chem 2011. [DOI: 10.1002/ejoc.201001581] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Yamada H, Kitauchi Y, Tanabe K, Ito T, Nishimoto SI. Anthraquinone-sensitized photooxidation of 5-methylcytosine in DNA leading to piperidine-induced efficient strand cleavage. Chemistry 2011; 17:2225-35. [PMID: 21294186 DOI: 10.1002/chem.201001884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Indexed: 11/10/2022]
Abstract
One-electron photooxidations of 5-methyl-2'-deoxycytidine (d(m)C) and 5-trideuteriomethyl-2'-deoxycytidine ([D(3)]d(m)C) by sensitization with anthraquinone (AQ) derivatives were investigated. Photoirradiation of an aerated aqueous solution containing d(m)C and anthraquinone 2-sulfonate (AQS) afforded 5-formyl-2'-deoxycytidine (d(f)C) and 5-hydroxymethyl-2'-deoxycytidine (d(hm)C) in good yield through an initial one-electron oxidation process. The deuterium isotope effect on the AQS-sensitized photooxidation of d(m)C suggests that the rate-determining step in the photosensitized oxidation of d(m)C involves internal transfer of the C5-hydrogen atom of a d(m)C-tetroxide intermediate to produce d(f)C and d(hm)C. In the case of a 5-methylcytosine ((m)C)-containing duplex DNA with an AQ chromophore that is incorporated into the backbone of the DNA strand so as to be immobilized at a specific position, (m)C underwent efficient direct one-electron oxidation by the photoexcited AQ, which resulted in an exclusive DNA strand cleavage at the target (m)C site upon hot piperidine treatment. In accordance with the suppression of the strand cleavage at 5-trideuterio-methylcytosine observed in a similar AQ photosensitization, it is suggested that deprotonation at the C5-methyl group of an intermediate (m)C radical cation may occur as a key elementary reaction in the photooxidative strand cleavage at the (m)C site. Incorporation of an AQ sensitizer into the interior of a strand of the duplex enhanced the one-electron photooxidation of (m)C, presumably because of an increased intersystem crossing efficiency that may lead to efficient piperidine-induced strand cleavage at an (m)C site in a DNA duplex.
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Affiliation(s)
- Hisatsugu Yamada
- Advanced Biomedical Engineering Research Unit, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8510, Japan.
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Tanabe K, Yamada H, Nishimoto SI. Preparation of Functionalized Oligodeoxynucleotides and Photochemical One-electron Oxidation of 5-Methylcytosine in DNA. J SYN ORG CHEM JPN 2011. [DOI: 10.5059/yukigoseikyokaishi.69.814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Münzel M, Lercher L, Müller M, Carell T. Chemical discrimination between dC and 5MedC via their hydroxylamine adducts. Nucleic Acids Res 2010; 38:e192. [PMID: 20813757 PMCID: PMC2995083 DOI: 10.1093/nar/gkq724] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The presence of the methylated nucleobase 5MedC in CpG islands is a key factor that determines gene silencing. False methylation patterns are responsible for deteriorated cellular development and are a hallmark of many cancers. Today genes can be sequenced for the content of 5MedC only with the help of the bisulfite reagent, which is based exclusively on chemical reactivity differences established by the additional methyl group. Despite intensive optimization of the bisulfite protocol, the method still has specificity problems. Most importantly ∼95% of the DNA analyte is degraded during the analysis procedure. We discovered that the reagent O-allylhydroxylamine is able to discriminate between dC and 5MedC. The reagent, in contrast to bisulfite, does not exploit reactivity differences but gives directly different reaction products. The reagent forms a stable mutagenic adduct with dC, which can exist in two states (E versus Z). In case of dC the allylhydroxylamine adduct switches into the E-isomeric form, which generates dC to dT transition mutations that can easily be detected by established methods. Significantly, the 5MedC-adduct adopts exclusively the Z-isomeric form, which causes the polymerase to stop. O-allylhydroxylamine does allow differentiation between dC and 5MedC with high accuracy, leading towards a novel and mild chemistry for methylation analysis.
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Affiliation(s)
- Martin Münzel
- Department of Chemistry, Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Butenandtstr. 5-13, 81377 Munich, Germany
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Dohno C, Shibata T, Nakatani K. Discrimination of N6-methyl adenine in a specific DNA sequence. Chem Commun (Camb) 2010; 46:5530-2. [DOI: 10.1039/c0cc00172d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Motorin Y, Lyko F, Helm M. 5-methylcytosine in RNA: detection, enzymatic formation and biological functions. Nucleic Acids Res 2009; 38:1415-30. [PMID: 20007150 PMCID: PMC2836557 DOI: 10.1093/nar/gkp1117] [Citation(s) in RCA: 240] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The nucleobase modification 5-methylcytosine (m5C) is widespread both in DNA and different cellular RNAs. The functions and enzymatic mechanisms of DNA m5C-methylation were extensively studied during the last decades. However, the location, the mechanism of formation and the cellular function(s) of the same modified nucleobase in RNA still remain to be elucidated. The recent development of a bisulfite sequencing approach for efficient m5C localization in various RNA molecules puts ribo-m5C in a highly privileged position as one of the few RNA modifications whose detection is amenable to PCR-based amplification and sequencing methods. Additional progress in the field also includes the characterization of several specific RNA methyltransferase enzymes in various organisms, and the discovery of a new and unexpected link between DNA and RNA m5C-methylation. Numerous putative RNA:m5C-MTases have now been identified and are awaiting characterization, including the identification of their RNA substrates and their related cellular functions. In order to bring these recent exciting developments into perspective, this review provides an ordered overview of the detection methods for RNA methylation, of the biochemistry, enzymology and molecular biology of the corresponding modification enzymes, and discusses perspectives for the emerging biological functions of these enzymes.
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Affiliation(s)
- Yuri Motorin
- Laboratoire ARN-RNP Maturation-Structure-Fonction, Enzymologie Moléculaire et Structurale (AREMS), UMR 7214 CNRS-UHP Faculté des Sciences et Techniques, Université Henri Poincaré, Nancy 1, Bld des Aiguillettes, BP 70239, 54506 Vandoeuvre-les-Nancy, France
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Interindividual variation in epigenomic phenomena in humans. Mamm Genome 2009; 20:604-11. [PMID: 19763687 DOI: 10.1007/s00335-009-9219-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2009] [Accepted: 08/18/2009] [Indexed: 12/20/2022]
Abstract
Our knowledge of regulatory mechanisms of gene expression and other chromosomal processes related to DNA methylation and chromatin state is continuing to grow at a rapid pace. Understanding how these epigenomic phenomena vary between individuals will have an impact on understanding their broader role in determining variation in gene expression and biochemical, physiological, and behavioural phenotypes. In this review we survey recent progress in this area, focusing on data available from humans. We highlight the role of obligatory (sequence-dependent) epigenomic variation as an important mechanism for generating interindividual variation that could impact our understanding of the mechanistic basis of complex trait architecture.
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Li M, Chen WD, Papadopoulos N, Goodman SN, Bjerregaard NC, Laurberg S, Levin B, Juhl H, Arber N, Moinova H, Durkee K, Schmidt K, He Y, Diehl F, Velculescu VE, Zhou S, Diaz LA, Kinzler KW, Markowitz SD, Vogelstein B. Sensitive digital quantification of DNA methylation in clinical samples. Nat Biotechnol 2009; 27:858-63. [PMID: 19684580 DOI: 10.1038/nbt.1559] [Citation(s) in RCA: 284] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Accepted: 07/27/2009] [Indexed: 12/14/2022]
Abstract
Analysis of abnormally methylated genes is increasingly important in basic research and in the development of cancer biomarkers. We have developed methyl-BEAMing technology to enable absolute quantification of the number of methylated molecules in a sample. Individual DNA fragments are amplified and analyzed either by flow cytometry or next-generation sequencing. We demonstrate enumeration of as few as one methylated molecule in approximately 5,000 unmethylated molecules in DNA from plasma or fecal samples. Using methylated vimentin as a biomarker in plasma samples, methyl-BEAMing detected 59% of cancer cases. In early-stage colorectal cancers, this sensitivity was four times more than that obtained by assaying serum-carcinoembryonic antigen (CEA). With stool samples, methyl-BEAMing detected 41% of cancers and 45% of advanced adenomas. In addition to diagnostic and prognostic applications, this digital quantification of rare methylation events should be applicable to preclinical assessment of new epigenetic biomarkers and quantitative analyses in epigenetic research.
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Affiliation(s)
- Meng Li
- The Ludwig Center for Cancer Genetics and Therapeutics, Howard Hughes Medical Institute and Sidney Kimmel Cancer Center at the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
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Nomura A, Tainaka K, Okamoto A. Osmium Complexation of Mismatched DNA: Effect of the Bases Adjacent to Mismatched 5-Methylcytosine. Bioconjug Chem 2009; 20:603-7. [DOI: 10.1021/bc800531z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Akiko Nomura
- Advanced Science Institute, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama 351-1098, Japan
| | - Kazuki Tainaka
- Advanced Science Institute, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama 351-1098, Japan
| | - Akimitsu Okamoto
- Advanced Science Institute, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama 351-1098, Japan
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Ogino M, Taya Y, Fujimoto K. Detection of methylcytosine by DNA photoligation via hydrophobic interaction of the alkyl group. Org Biomol Chem 2009. [DOI: 10.1039/b904941j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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