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Vol. 10, Issue 11, 1697-1710, November 2000
Sequence and Comparative Analysis of the Mouse 1-Megabase Region Orthologous to the Human 11p15 Imprinted Domain
Patrick
Onyango,1,2
Webb
Miller,3
Jessica
Lehoczky,4
Cheuk T.
Leung,1,5
Bruce
Birren,4
Sarah
Wheelan,5,7
Ken
Dewar,4 and
Andrew P.
Feinberg1,2,5,6,8
1 Institute of Genetic Medicine and 2 Department
of Medicine, Johns Hopkins University School of Medicine, Baltimore,
Maryland 21205, USA; 3 Department of Computer Science and
Engineering, Pennsylvania State University, University Park,
Pennsylvania 16802, USA; 4 Whitehead Institute/MIT Center for
Genome Research, Cambridge, Massachusetts 02141, USA;
5 Department of Molecular Biology and Genetics and
6 Department of Oncology, Johns Hopkins University School of
Medicine, Baltimore, Maryland 21205, USA; 7 Center for
Biotechnology Information, National Institutes of Health, Bethesda,
Maryland 20894, USA
A major barrier to conceptual advances in understanding the
mechanisms and regulation of imprinting of a genomic region is our
relatively poor understanding of the overall organization of genes and
of the potentially important cis-acting regulatory sequences
that lie in the nonexonic segments that make up 97% of the genome.
Interspecies sequence comparison offers an effective approach to
identify sequence from conserved functional elements. In this article
we describe the successful use of this approach in comparing a ~1-Mb
imprinted genomic domain on mouse chromosome 7 to its orthologous
region on human 11p15.5. Within the region, we identified 112 exons of
known genes as well as a novel gene identified uniquely in the mouse
region, termed Msuit, that was found to be imprinted. In
addition to these coding elements, we identified 33 CpG islands and 49 orthologous nonexonic, nonisland sequences that met our criteria as
being conserved, and making up 4.1% of the total sequence. These
conserved noncoding sequence elements were generally clustered near
imprinted genes and the majority were between Igf2 and
H19 or within Kvlqt1. Finally, the location of CpG
islands provided evidence that suggested a two-island rule for
imprinted genes. This study provides the first global view of the
architecture of an entire imprinted domain and provides candidate
sequence elements for subsequent functional analyses.
[The
sequence data described in this paper have been submitted to the
GenBank data library under accession nos. AF313042 to AF313150.]
8
Corresponding author.
10:1697-1710 ©2000 by Cold Spring Harbor Laboratory Press ISSN 1088-9051/00 $5.00
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