title: An assessment of the role of DNA adenine methyltransferase on gene expression regulation in E coli.
abstract: N6-Adenine methylation is an important epigenetic signal, which regulates various processes, such as DNA replication and repair and transcription. In gamma-proteobacteria, Dam is a stand-alone enzyme that methylates GATC sites, which are non-randomly distributed in the genome. Some of these overlap with transcription factor binding sites. This work describes a global computational analysis of a published Dam knockout microarray alongside other publicly available data to throw insights into the extent to which Dam regulates transcription by interfering with protein binding. The results indicate that DNA methylation by DAM may not globally affect gene transcription by physically blocking access of transcription factors to binding sites. Down-regulation of Dam during stationary phase correlates with the activity of TFs whose binding sites are enriched for GATC sites.
authors.affiliation: Genomics and Regulatory Systems Group, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom. aswin@ebi.ac.uk
authors.forename: Aswin Sai Narain
authors.initials: AS
authors.lastname: Seshasayee
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D015536:Down-Regulation; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000235:genetics* / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D009838:Oligodeoxyribonucleotides; D014157:Transcription Factors; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific)