title: ["Co-phased blocks"--conservative regions of double-stranded DNA of transcriptional regulatory modules--are close in space due to phasing at nucleosome DNA super helix].
abstract: Conservative regions varying in length from 30 to 70 nucleotides (nt) are revealed as a result of interspecies comparison of homologous nucleotide sequences of the loci, genes controlling early development in Drosophila species. These regions are observed at the intermediate level between transcription factor binding sites (usually about 7-10 nt) and the nucleosome repeat unit (165-210 nt). Segments found are located mainly in the area of known functional elements of the locus (cis-regulatory modules: enhancers, a proximal promoter, a coding segment). Conservative domains occupy less than a half of the full enhancer length and contain practically all annotated transcription factor binding sites. A quasi periodical pattern of conservative region disposition is in accord with the experimental nucleosome localization pattern. The distance between neighboring domains is about 84 nt, i.e. a pitch of nucleosome DNA super helix. A repeatable accuracy of the distance permits of treating the delineated conservative regions as co-phased blocks and stating that these domains are close in the space being located at neighboring coils of the nucleosome DNA super helix.
authors: A P
authors: AP
authors: Lifanov
authors: V Iu
authors: VIu
authors: Makeev
authors: N G
authors: NG
authors: Esipova
mesh_terms: D000818:Animals; D004278:DNA, Superhelical / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004330:Drosophila; D029721:Drosophila Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D009707:Nucleosomes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic / Q000502:physiology*
chemical_list: D004278:DNA, Superhelical; D029721:Drosophila Proteins; D009707:Nucleosomes