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

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

Departments of ^*Genetics and ^‡Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520; and ^§Department of Genetics, Case Western Reserve University School of Medicine and Center for Human Genetics, University Hospitals of Cleveland, Cleveland, OH 44106

Communicated by Francis H. Ruddle, Yale University, New Haven, CT (received for review February 18, 1999)

Abstract

Nuclear matrix binding assays (NMBAs) define certain DNA sequences as matrix attachment regions (MARs), which often have cis-acting epigenetic regulatory functions. We used NMBAs to analyze the functionally important 15q11-q13 imprinting center (IC). We find that the IC is composed of an unusually high density of MARs, located in close proximity to the germ line elements that are proposed to direct imprint switching in this region. Moreover, we find 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 usually associated with genes but rather with heterochromatin-forming areas of the genome. In contrast, the 15q11-q13 region contains multiple transcribed genes and is unusual for being subject to genomic imprinting, causing the maternal chromosome to be more transcriptionally silent, methylated, and late replicating than the paternal chromosome. We suggest that the extensive MAR sequences at the IC are organized as heterochromatin during oogenesis, an organization disrupted during spermatogenesis. Consistent with this model, multicolor fluorescence in situ hybridization to halo nuclei demonstrates a strong matrix association of the maternal IC, whereas the paternal IC is more decondensed, extending into the nuclear halo. This model also provides a mechanism for spreading of the imprinting signal, because heterochromatin 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 identified in this study.

Footnotes

↵ † To whom reprint requests should be addressed. E-mail john.greally{at}yale.edu.
Data deposition: The sequences reported in this paper have been deposited in the GenBank database [accession nos. AF130843 (5′Snrpn, 6.8 kb), AF130844 (5′ ZNF127, 6.2 kb), and AF130348 (5′ Zfp127, 7.2 kb).].
Abbreviations:

AS,

Angelman syndrome;

FISH,

fluorescence in situ hybridization;

IC,

imprinting center;

IM,

imprinting mutation;

MAR,

matrix attachment region;

NMBA,

nuclear matrix binding assay;

ORE,

oogenesis-responsive element;

PWS,

Prader–Willi syndrome;

SNRPN, small nuclear ribonucleoprotein N,

SNURF, SNRPN upstream reading frame;

ZNF127/Zfp127,

zinc finger protein 127