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      Modified Nucleotides for Discrimination between Cytosine and the Epigenetic Marker 5‐Methylcytosine

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          Abstract

          5‐Methyl‐2′‐deoxycytosine, the most common epigenetic marker of DNA in eukaryotic cells, plays a key role in gene regulation and affects various cellular processes such as development and carcinogenesis. Therefore, the detection of 5mC can serve as an important biomarker for diagnostics. Here we describe that modified dGTP analogues as well as modified primers are able to sense the presence or absence of a single methylation of C, even though this modification does not interfere directly with Watson–Crick nucleobase pairing. By screening several modified nucleotide scaffolds, O 6‐modified 2′‐deoxyguanosine analogues were identified as discriminating between C and 5mC. These modified nucleotides might find application in site‐specific 5mC detection, for example, through real‐time PCR approaches.

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          Induced pluripotent stem cell lines derived from human somatic cells.

          Junying Yu, Maxim A Vodyanik, Kim Smuga-Otto … (2007)
          Somatic cell nuclear transfer allows trans-acting factors present in the mammalian oocyte to reprogram somatic cell nuclei to an undifferentiated state. We show that four factors (OCT4, SOX2, NANOG, and LIN28) are sufficient to reprogram human somatic cells to pluripotent stem cells that exhibit the essential characteristics of embryonic stem (ES) cells. These induced pluripotent human stem cells have normal karyotypes, express telomerase activity, express cell surface markers and genes that characterize human ES cells, and maintain the developmental potential to differentiate into advanced derivatives of all three primary germ layers. Such induced pluripotent human cell lines should be useful in the production of new disease models and in drug development, as well as for applications in transplantation medicine, once technical limitations (for example, mutation through viral integration) are eliminated.
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            DNA methylation: bisulphite modification and analysis.

            Marianne Frommer, Clare Stirzaker, Melody Clark … (2005)
            DNA methylation is an important epigenetic modification of DNA in mammalian genomes. DNA methylation patterns are established early in development, modulated during tissue-specific differentiation and disrupted in many disease states, including cancer. To understand further the biological functions of these changes, accurate and reproducible methods are required to fully analyze the DNA methylation sequence. Here, we describe the 'gold-standard' bisulphite conversion protocol that can be used to re-sequence DNA from mammalian cells in order to determine and quantify the methylation state of a gene or genomic region at single-nucleotide resolution. The process of bisulphite treatment exploits the different sensitivities of cytosine and 5-methylcytosine (5-MeC) to deamination by bisulphite under acidic conditions--in which cytosine undergoes conversion to uracil, whereas 5-MeC remains unreactive. Bisulphite conversion of DNA, in either single tubes or in a 96-well format, can be performed in a minimum of 8 h and a maximum of 18 h, depending on the amount and quality of starting DNA.
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              Purification of CpG islands using a methylated DNA binding column.

              X Nan, S. Cross, Joanna J. Charlton … (1994)
              CpG islands are short stretches of DNA containing a high density of non-methylated CpG dinucleotides, predominantly associated with coding regions. We have constructed an affinity matrix that contains the methyl-CpG binding domain from the rat chromosomal protein MeCP2, attached to a solid support. A column containing the matrix fractionates DNA according to its degree of CpG methylation, strongly retaining those sequences that are highly methylated. Using this column, we have developed a procedure for bulk isolation of CpG islands from human genomic DNA. As CpG islands overlap with approximately 60% of human genes, the resulting CpG island library can be used to isolate full-length cDNAs and to place genes on genomic maps.
              Article 0 comments Cited 79 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Prof. Dr. Andreas Marx: andreas.marx@uni-konstanz.de
                Journal
                Journal ID (nlm-ta): Angew Chem Int Ed Engl
                Journal ID (iso-abbrev): Angew. Chem. Int. Ed. Engl
                Journal ID (doi): 10.1002/(ISSN)1521-3773
                Journal ID (publisher-id): ANIE
                Title: Angewandte Chemie (International Ed. in English)
                Publisher: John Wiley and Sons Inc. (Hoboken )
                ISSN (Print): 1433-7851
                ISSN (Electronic): 1521-3773
                Publication date (Electronic): 02 February 2016
                Publication date (Print): 24 February 2016
                Volume: 55
                Issue: 9 ( doiID: 10.1002/anie.v55.9 )
                Pages: 3229-3232
                Affiliations
                [ 1 ] Fachbereich Chemie, Graduiertenschule Chemische, Biologie KonstanzUniversität Konstanz Universitätsstrasse 10 78457 KonstanzDeutschland
                Author notes
                [†]

                These authors contributed equally to this work.

                Article
                Publisher ID: ANIE201511520
                DOI: 10.1002/anie.201511520
                PMC ID: 4949677
                PubMed ID: 26835661
                SO-VID: d2b5d530-54bb-42de-83a4-d405372c9ff1
                Copyright © © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.
                License:

                This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 11 December 2015
                Page count
                Figures: 6, Tables: 1, References: 45, Pages: 4
                Funding
                Funded by: European Research Council
                Funded by: ERC
                Award ID: 339834
                Categories
                Subject: Communication
                Subject: Communications
                Subject: Epigenetics
                Custom metadata
                source-schema-version-number 2.0
                component-id anie201511520
                cover-date February 24, 2016
                details-of-publishers-convertor Converter:WILEY_ML3GV2_TO_NLMPMC version:4.9.2 mode:remove_FC converted:19.07.2016

                ScienceOpen disciplines: Chemistry
                Keywords: 5-methylcytosine,dna methylation,dna polymerase,epigenetics,polymerase chain reaction
                Data availability:
                ScienceOpen disciplines: Chemistry
                Keywords: 5-methylcytosine, dna methylation, dna polymerase, epigenetics, polymerase chain reaction

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