Three copies of a highly repetitive DNA sequence B1 which is complementary to the most abundant class of mouse fold-back RNA have been cloned in pBR322 plasmid and sequenced by the method of Maxam and Gilbert. All the three have a length of about 130 base pairs and are very similar in their base sequence. The deviation from the average sequence is equal to 4% and the overall mismatch between each two is not higher than 8%, One of the recombinant clones used contained two copies of B1 oriented in the same direction. All of the B1 copies are flanked with sequences which possess nonidentical but very similar structure. They consist of a number of A_mC_n blocks (where m varies from 2 to 8 and n equals 1–2). These peculiar sequences in all cases are separated from B1 by non-homologous DNA stretches of 2–8 residues. In one case, a long polypurine stretch is located next to such a block. It consists of 74 residues most of which represent a reiteration of the basic sequence AAAAG. We have found two regions within the B1 sequence which are homologous to the intron-exon junctions, especially to those present in the large intron of the mouse β-globin gene. It may indicate the involvement of the B1 sequence in pre-mRNA splicing.

Mouse genome contains two major families of short interspersed repeats in more than 105 copies scattered throughout the whole genome. They are referred to as B1 and B2 sequences since they were first isolated from the genome Horary by means of a dsRNA-B probe /1/. In this work, two copies of the B2 family were sequenced and compared with the previously sequenced B1 repeat /2/. A B2 ubiquitous repeat is ca. 190 bp long. The members of the family deviate in 3–5% of nucleotides from the consensus sequence. B2 contains regions of homology to the RNA polymerase III split promoter and to 4.5S snENA I. Both B1 and B2 contain regions which resemble junctions between exons and introns. In contrast to B1, B2 does not contain apparent homologies to papova viral replication origins and a human Alu sequence. One side of the B2 repeat is represented by a very AT-rich sequence (ca. 30 bp long) followed with an oligo(dA) stretch 10–15 nucleotides long. This region of the repeat is the most variable one. The whole unit is flanked with 15–16 bp direct repeats different in sequenced copies of B2. The same is true of some copies of the B1 family. The properties of B1 and B2 repeats suggest that they may represent a novel class of transposon-like elements in eukaryctic genome. A possible role of B-type repeats in genome reorganization, DNA replication and pre-mRNA processing is discussed.

DNA preparations from about hundred randomly selected clones containing mouse DNA fragments were screened for the existence of sequences complementary to long double-stranded regions of pre-mRNA able to snap back after melting (dsRNA-B). Many clones containing such sequences were found. The cloned sequences can be subdivided into three groups: (1) those complementary to about a half (at least to 30-40%) of the total dsRNA, designated as sequences B1; (2) those complementary to a part of sequence B1; and (3) sequences complementary to about a quarter (at least to 15%) of the total dsRNA referred to as sequence B2. The size of DNA sequence complementary to dsRNA is about 400 base pairs. Melting experiments with hybrids show that the members of B1 family are very similar if not identical, while the divergence among B2 sequences is higher, but still the number of substitutions does not exceed 9% of bases. Thus, the major part of dsRNA-B consists of a small number of highly abundant sequences as was suggested earlier on the basis of renaturation kinetics /1-3/. Sequences B1 and B2 are represented by many copies in the mouse genome and in pre-mRNA, and many of them probably do not form hairpin-like structures.

Detailed reviews describing work presented at the annual Cold Spring Harbor Symposia on Quantitative Biology