No abstract

SINEBase (http://sines.eimb.ru) integrates the revisited body of knowledge about short interspersed elements (SINEs). A set of formal definitions concerning SINEs was introduced. All available sequence data were screened through these definitions and the genetic elements misidentified as SINEs were discarded. As a result, 175 SINE families have been recognized in animals, flowering plants and green algae. These families were classified by the modular structure of their nucleotide sequences and the frequencies of different patterns were evaluated. These data formed the basis for the database of SINEs. The SINEBase website can be used in two ways: first, to explore the database of SINE families, and second, to analyse candidate SINE sequences using specifically developed tools. This article presents an overview of the database and the process of SINE identification and analysis.

Mouse genome contains two major families of short interspersed repeats in more than 10(5) copies scattered throughout the whole genome. They are referred to as B1 and B2 sequences since they were first isolated from the genome library 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 snRNA 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 eukaryotic genome. A possible role of B-type repeats in genome reorganization, DNA replication and pre-mRNA processing is discussed.

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 AmCn 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 beta-globin gene. It may indicate the involvement of the B1 sequence in pre-mRNA splicing.

Two cell lines originating from a common ancestral tumor, CSML0 and CSML100, were used as a model to study AP-1 transcription factors at different steps of tumor progression. CSML0 cells have an epithelial morphology; they express epithelial but not mesenchymal markers and are invasive neither in vitro nor in vivo. CSML100 possesses all characteristics of a highly progressive carcinoma. These cells do not form tight contacts, are highly invasive in vitro, and are metastatic in vivo. AP-1 activity was considerably higher in CSML100 cells than in CSML0 cells. There was a common predominant Jun component, namely, JunD, detected in both cell lines. We found that the enhanced level of AP-1 in CSML100 cells was due to high expression of Fra-1 and Fra-2 proteins, which were undetectable in CSML0 nuclear extracts. Analysis of the transcription of different AP-1 members in various cell lines derived from tumors of epithelial origin revealed a correlation of fra-1 expression with mesenchymal characteristics of carcinoma cells. Moreover, we show here for the first time that the expression of exogenous Fra-1 in epithelioid cells results in morphological changes that resemble fibroblastoid conversion. Cells acquire an elongated shape and become more motile and invasive in vitro. Morphological alterations were accompanied by transcriptional activation of certain genes whose expression is often induced at late stages of tumor progression. These data suggest a critical role of the Fra-1 protein in the development of epithelial tumors.