DNA methylation is a covalent modification of the nucleotide cytosine that is 
stably inherited at the dinucleotide CpG by somatic cells, and 70% of CpG 
dinucleotides in the genome are methylated. The exception to this pattern of 
methylation are CpG islands, CpG-rich sequences that are protected from 
methylation, and generally are thought to be methylated only on the inactive 
X-chromosome and in tumors, as well as differentially methylated regions (DMRs) 
in the vicinity of imprinted genes. To identify chromosomal regions that might 
harbor imprinted genes, we devised a strategy for isolating a library of 
normally methylated CpG islands. Most of the methylated CpG islands represented 
high copy number dispersed repeats. However, 62 unique clones in the library 
were characterized, all of which were methylated and GC-rich, with a GC content 
>50%. Of these, 43 clones also showed a CpG(obs)/CpG(exp) >0.6, of which 30 were 
studied in detail. These unique methylated CpG islands mapped to 23 chromosomal 
regions, and 12 were differentially methylated regions in uniparental tissues of 
germline origin, i.e., hydatidiform moles (paternal origin) and complete ovarian 
teratomas (maternal origin), even though many apparently were methylated in 
somatic tissues. We term these sequences gDMRs, for germline differentially 
methylated regions. At least two gDMRs mapped near imprinted genes, HYMA1 and a 
novel homolog of Elongin A and Elongin A2, which we term Elongin A3. 
Surprisingly, 18 of the methylated CpG islands were methylated in germline 
tissues of both parental origins, representing a previously uncharacterized 
class of normally methylated CpG islands in the genome, and which we term 
similarly methylated regions (SMRs). These SMRs, in contrast to the gDMRs, were 
significantly associated with telomeric band locations (P =.0008), suggesting a 
potential role for SMRs in chromosome organization. At least 10 of the 
methylated CpG islands were on average 85% conserved between mouse and human. 
These sequences will provide a valuable resource in the search for novel 
imprinted genes, for defining the molecular substrates of the normal methylome, 
and for identifying novel targets for mammalian chromatin formation.