Most highly repeated dispersed DNA families in the mouse genome.

Abstract

The construction of a small library of mouse repetitive DNA has been previously reported (Pietras et al., Nucleic Acids Res. 11:6965-6983, 1983). Here we report that the 35 plasmids in this library corresponding to highly repeated (>30,000 copies per genome) dispersed DNA sequences can be grouped into no more than 5 distinct families. These families together comprise 8 to 10% of the mouse genome. They include the previously described small elements Bi, B2, and R and the large MIF-1 element. Twelve of the 35 clones contain evolutionarily conserved (EC) sequences. One EC clone in our library mostly consists of alternating dCdT residues; another consists of tandem repeats of the sequence CCTCT. The majority of Bls and B2s in the genome appear to be homogeneous, whereas R sequences, ECs, and MIF-is are heterogeneous. Two earlier reports showed highly repeated mammalian DNA sequences in the herpesvirus genome (Peden et al., Cell 31:71-80, 1982; Puga et al., Cell 31:81-87, 1982). We show that sequences homologous to our EC clones are present in the herpesvirus genome, although these polypyrimidine stretches are not detected in poxvirus, adenovirus, and simian virus 40 genomes. We detect transcripts containing homology to all of these sequences in a nuclear transcription assay. Also, we show that small, polyadenylated RNA molecules homologous to B2 sequences are expressed in undifferentiated embryonal carcinoma cells but not in their differentiated derivatives. The significance of these findings is discussed.Several highly repeated, nonsatellite families of DNA sequences have been reported in the mouse (51). These include the following: Bi, which is the mouse Alu (30) equivalent (32); B2 (33); MIF-1, the mouse interspersed fragment, originally called the 1.3-kilobase (kb) EcoRI fragment but now known to be greater than 5 kb in its entirety (13,14,26,42); the R sequence, a 400-to 500-base-pair (bp)-size family first located in multiple copies amidst the immunoglobulin cluster (20, 35); and EC1, an evolutionarily conserved (EC) sequence described in humans and mice (2, 41). EC1 is conserved in all eucaryotes, including yeast cells, so its hybridization to mammalian DNA is reduced considerably if unlabeled eucaryotic DNA is used as a carrier in the experiments.It is our prejudice that each repetitive sequence family will be found to have a very different role and history in the mouse genome, and as such, one cannot consider repetitive DNA in bulk in terms of functional versus selfish roles (17, 43). Therefore, we and others (52) containing clones) of repetitive genomic DNA (48). This library, being randomly generated, is representative of the entire genome and contains several cloned sequences corresponding to each of the most repeated (>30,000 copies) DNA families. As our library should contain a representative of every family repeated more than 20,000 to 30,000 times, we have an opportunity to sort out how many highly repeated families exist in the mouse genome. These are of particular interest because presumably the...

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