Conserved characteristics of heterochromatin-forming DNA at the 15q11-q13 imprinting center

Nuclear matrix binding assays (NMBAs) define certain DNA sequences as matri x attachment regions (MARs), which often have cis-acting epigenetic regulat ory functions. We used NMBA5 to analyze the functionally important 15q11-q1 3 imprinting center (IC). We find that the IC is composed of an unusually h igh density of MARs, located in close proximity to the germ line elements t hat are proposed to direct imprint switching in this region. Moreover, we f ind that the organization of MARs is the same at the homologous mouse locus , despite extensive divergence of DNA sequence. MARs of this size are not u sually associated with genes but rather with heterochromatin-forming areas of the genome, In contrast, the 15q11-q13 region contains multiple transcri bed genes and is unusual for being subject to genomic imprinting, causing t he maternal chromosome to be more transcriptionally silent, methylated, and late replicating than the paternal chromosome We suggest that the extensiv e MAR sequences at the IC are organized as heterochromatin during oogenesis , an organization disrupted during spermatogenesis. Consistent with this mo des, multicolor fluorescence in situ hybridization to halo nuclei demonstra tes a strong matrix association of the maternal IC, whereas the paternal IC is more decondensed, extending into the nuclear halo, This model also prov ides a mechanism for spreading of the imprinting signal, because heterochro matin at the IC on the maternal chromosome may exert a suppressive position effect in cis, We propose that the germ line elements at the 15q11-q13 IC mediate their effects through the candidate heterochromatin-forming DNA ide ntified in this study.