Specific association between type-II intracisternal A-particle elements and other repetitive sequences in the mouse genome.

The majority of type-II intracisternal A-particle (IAP) element clones isolated from a mouse genomic library also contained highly repetitive DNA sequences in addition to the moderately repetitive IAP elements. Further analysis revealed that eleven of the twelve clones contained sequences of the mouse L1 family. One clone contained four copies of a limited region of the 3' end of the L1 element in a 12-kb stretch of sequence. This clone also contained a newly identified repetitive sequence which is found associated with type-II IAP elements. Type-II IAP elements were completely methylated in mouse embryo DNA; in myeloma cells, partial demethylation of the sequences correlated with known transcriptional activity of the IAP subclasses. Analysis of genomic DNA showed that association with other repetitive sequences appears to be a general property of many type-II IAP elements and may reflect their location in a particular chromosomal environment.