Direct detection of methylation in genomic DNA
The identification of methylated sites on bacterial genomic DNA would be a useful tool to study the major roles of DNA methylation in prokaryotes: distinction of self and nonself DNA, direction of post-replicative mismatch repair, control of DNA replication and cell cycle, and regulation of gene exp...
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| Veröffentlicht in: | Nucleic acids research 2005-01, Vol.33 (14), p.e124-e124 |
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| container_title | Nucleic acids research |
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| creator | Bart, A. van Passel, M. W. J. van Amsterdam, K. van der Ende, A. |
| description | The identification of methylated sites on bacterial genomic DNA would be a useful tool to study the major roles of DNA methylation in prokaryotes: distinction of self and nonself DNA, direction of post-replicative mismatch repair, control of DNA replication and cell cycle, and regulation of gene expression. Three types of methylated nucleobases are known: N6-methyladenine, 5-methylcytosine and N4-methylcytosine. The aim of this study was to develop a method to detect all three types of DNA methylation in complete genomic DNA. It was previously shown that N6-methyladenine and 5-methylcytosine in plasmid and viral DNA can be detected by intersequence trace comparison of methylated and unmethylated DNA. We extended this method to include N4-methylcytosine detection in both in vitro and in vivo methylated DNA. Furthermore, application of intersequence trace comparison was extended to bacterial genomic DNA. Finally, we present evidence that intrasequence comparison suffices to detect methylated sites in genomic DNA. In conclusion, we present a method to detect all three natural types of DNA methylation in bacterial genomic DNA. This provides the possibility to define the complete methylome of any prokaryote. |
| doi_str_mv | 10.1093/nar/gni121 |
| format | Article |
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Furthermore, application of intersequence trace comparison was extended to bacterial genomic DNA. Finally, we present evidence that intrasequence comparison suffices to detect methylated sites in genomic DNA. In conclusion, we present a method to detect all three natural types of DNA methylation in bacterial genomic DNA. 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J.</creatorcontrib><creatorcontrib>van Amsterdam, K.</creatorcontrib><creatorcontrib>van der Ende, A.</creatorcontrib><title>Direct detection of methylation in genomic DNA</title><title>Nucleic acids research</title><addtitle>Nucl. Acids Res</addtitle><description>The identification of methylated sites on bacterial genomic DNA would be a useful tool to study the major roles of DNA methylation in prokaryotes: distinction of self and nonself DNA, direction of post-replicative mismatch repair, control of DNA replication and cell cycle, and regulation of gene expression. Three types of methylated nucleobases are known: N6-methyladenine, 5-methylcytosine and N4-methylcytosine. The aim of this study was to develop a method to detect all three types of DNA methylation in complete genomic DNA. It was previously shown that N6-methyladenine and 5-methylcytosine in plasmid and viral DNA can be detected by intersequence trace comparison of methylated and unmethylated DNA. We extended this method to include N4-methylcytosine detection in both in vitro and in vivo methylated DNA. Furthermore, application of intersequence trace comparison was extended to bacterial genomic DNA. Finally, we present evidence that intrasequence comparison suffices to detect methylated sites in genomic DNA. In conclusion, we present a method to detect all three natural types of DNA methylation in bacterial genomic DNA. 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J. ; van Amsterdam, K. ; van der Ende, A.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c472t-a5bc83f0e75fbf790db4a0815d9b375f90fbdf2b757f2354dd57a585253c617e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>5-Methylcytosine - analysis</topic><topic>Adenine - analogs & derivatives</topic><topic>Adenine - analysis</topic><topic>Cytosine - analogs & derivatives</topic><topic>Cytosine - analysis</topic><topic>Deoxyguanine Nucleotides - metabolism</topic><topic>Dideoxynucleotides</topic><topic>DNA Methylation</topic><topic>DNA, Bacterial - chemistry</topic><topic>DNA, Bacterial - metabolism</topic><topic>Genome, Bacterial</topic><topic>Genomics - methods</topic><topic>Methods Online</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Bart, A.</creatorcontrib><creatorcontrib>van Passel, M. W. 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W. J.</au><au>van Amsterdam, K.</au><au>van der Ende, A.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Direct detection of methylation in genomic DNA</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucl. Acids Res</addtitle><date>2005-01-01</date><risdate>2005</risdate><volume>33</volume><issue>14</issue><spage>e124</spage><epage>e124</epage><pages>e124-e124</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><coden>NARHAD</coden><abstract>The identification of methylated sites on bacterial genomic DNA would be a useful tool to study the major roles of DNA methylation in prokaryotes: distinction of self and nonself DNA, direction of post-replicative mismatch repair, control of DNA replication and cell cycle, and regulation of gene expression. Three types of methylated nucleobases are known: N6-methyladenine, 5-methylcytosine and N4-methylcytosine. 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| subjects | 5-Methylcytosine - analysis Adenine - analogs & derivatives Adenine - analysis Cytosine - analogs & derivatives Cytosine - analysis Deoxyguanine Nucleotides - metabolism Dideoxynucleotides DNA Methylation DNA, Bacterial - chemistry DNA, Bacterial - metabolism Genome, Bacterial Genomics - methods Methods Online |
| title | Direct detection of methylation in genomic DNA |
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