Nucleosome positioning signals and potential H–DNA within the DNA sequence of the imprinting control region of the mouse Igf2r gene

Abstract

The imprinting control region within the second intron of the mouse Igf2r gene contains a CpG island comprising direct repeats, an imprinting box and the Air antisense promoter which is blocked by the methylation imprint on the active maternal allele. We have investigated the structural features of this DNA, including a mapping of all nucleosome positioning signals within the nucleotide sequence. A discrete series of strong positioning signals distinguished the direct repeat region from the much more diverse positioning capacity of the sequence encompassing the known regulatory elements. At only a few locations did CpG methylation modulate the use of this positioning information. Direct effects upon histone–DNA interactions are therefore unlikely to contribute significantly to the means by which the imprint may establish allele-specific chromatin architecture and determine Air expression. A strand-specific obstruction to DNA polymerase was observed between the repeat and regulatory regions. The same region adopts triple-stranded H–DNA structures in supercoiled DNA, according to pH and divalent cation exposure. Methylation did not modulate the occurrence or form of this structure under the conditions tested. This finding nevertheless adds to the repertoire of potential H–DNA structures found in the vicinity of regulatory sequences—here, in an imprinting context.