title: Dam methylase accessibility as an instrument for analysis of mammalian chromatin structure.
abstract: For a 140-kb human genome locus, an analysis of the distribution of Dam methylase accessible sites, DNase I sensitive and resistant regions, unmethylated CpG sites and acetylated histone H3 molecules was performed and compared with transcriptional activity of the genes within the locus. A direct correlation was found between the extent of Dam methylation and C5 cytosine (CpG) methylation. It was also demonstrated that promoter regions of all highly and moderately transcribed genes are highly accessible to methylation by Dam methylase. In contrast, promoters of non-transcribed genes showed a very low extent of Dam methylation. Promoter regions of non-transcribed genes were also highly CpG methylated, and the promoter and more distant 5'-regions of the housekeeping gene COX6B1 were substantially CpG-demethylated. Some highly Dam methylase accessible regions are present in the intergenic regions of the locus suggesting that the latter contain either unidentified non-coding transcripts or extended regulatory elements like locus control regions.
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Svetlana S
authors.initials: SS
authors.lastname: Bulanenkova
authors.forename: Alena A
authors.initials: AA
authors.lastname: Kozlova
authors.forename: Elena S
authors.initials: ES
authors.lastname: Kotova
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Snezhkov
authors.forename: Tatyana L
authors.initials: TL
authors.lastname: Azhikina
authors.forename: Sergey B
authors.initials: SB
authors.lastname: Akopov
authors.forename: Lev G
authors.initials: LG
authors.lastname: Nikolaev
authors.forename: Eugene D
authors.initials: ED
authors.lastname: Sverdlov
mesh_terms: D000107:Acetylation; D000818:Animals; D002843:Chromatin / Q000737:chemistry* / Q000235:genetics; D042002:Chromatin Assembly and Disassembly; D047369:Chromatin Immunoprecipitation; D002888:Chromosomes, Human, Pair 19 / Q000737:chemistry / Q000235:genetics; D018899:CpG Islands; D019175:DNA Methylation; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry; D003576:Electron Transport Complex IV / Q000737:chemistry / Q000235:genetics; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics; D056426:Genetic Loci; D015894:Genome, Human; D057809:HEK293 Cells; D006657:Histones / Q000235:genetics / Q000378:metabolism; D006801:Humans; D008322:Mammals / Q000235:genetics*; D010957:Plasmids / Q000737:chemistry / Q000235:genetics; D011401:Promoter Regions, Genetic; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000737:chemistry* / Q000235:genetics; D014158:Transcription, Genetic; D014162:Transfection
chemical_list: D002843:Chromatin; D006657:Histones; C513775:COX6B1 protein, human; D003576:Electron Transport Complex IV; C058693:Dam methyltransferase; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific); C020102:endodeoxyribonuclease DpnI; D015252:Deoxyribonucleases, Type II Site-Specific