Ubiquitous transposon-like repeats B1 and B2 of the mouse genome: B2 sequencing

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Abstract
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.