Maternal-specific footprints at putative CTCF sites in the H19 imprinting control region give evidence for insulator function

Parent-of-origin-specific expression of the mouse insulin-like growth facto r 2 (Igf2) gene and the closely linked H19 gene are regulated by an interve ning 2 kb imprinting control region (ICR), which displays parent-specific d ifferential DNA methylation [1,2]. Four 21 bp repeats are embedded within t he ICR and are conserved in the putative ICR of human and rat Igf2 and H19, suggesting that the repeats have a function [3,4]. Here, we report that pr ominent DNA footprints were found in vivo on the unmethylated maternal ICR at ail four 21 bp repeats, demonstrating the presence of protein binding. T he methylated paternal ICR displayed no footprints. Significantly, the mate rnal-specific footprints were localized to putative binding sites for CTCF, a highly conserved zinc-finger DNA-binding protein with multiple roles in gene regulation including that of chromatin insulator function [5,6]. These results strongly suggest that the maternal ICR functions as an insulator e lement in regulating mutually exclusive expression of Igf2 and H19 in cis.