Structural organization and DNA methylation patterning within the mouse L1 family

We have studied stable differences in patterns of DNA methylation seen in the repeated sequences of mouse cells. A cloned 1330-base pair fragment of mouse repetitive DNA (pFS-13) was used as a probe in Southern blotting experiments. Mouse spleen and L1210 lymphoma DNA appeared to be normally methylated at HpaII sites probed by this sequence. Friend erythroleukemia cell, and Sp2 cell DNA both showed an abnormal banding pattern in HpaII digests. Hybridization in situ to metaphase chromosomes showed that probed sequences were broadly interspersed along the arms of each mouse chromosome. The DNA sequence of the 1330-base pair insert in the clone was determined; a copy of the R sequence of L1 was found at its 5' end. Walking experiments using M13 subclones from pFS-13 permitted the construction of a map for d(pCCGG) sites at the 3' end of the mouse L1 family. The unmethylated d(pCCGG) sites in Sp2 and Friend cells could then be assigned to polymorphic-repeated sequence groups within L1, homologous to the region spanned by BAM5 and R. Since there are several thousand copies of each of the fragments seen in autoradiographs, these sequences must possess a common methylation state at many genomic locations. Concerted (nonrandom) hypomethylation of certain subfamilies of L1 appears to be a stable characteristic of several cell lineages. These findings suggest that certain L1 families possess commonalities that permit and perhaps require differential DNA methylation in established cell lineages.