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The highly conserved synovial sarcoma associated protein SS18 is thought to act as a transcriptional co-activator through interactions with various proteins involved in (epigenetic) gene regulation. The SS18 SNH domain appears to act as a major interface for these protein-protein interactions. Previously, we used this SNH domain to identify SS18 paralogs (SS18L1 and SS18L2) and orthologs in various species. The functional significance of these SS18-like proteins is embodied by the observations that SS18L1 and SS18L2 can replace SS18 in its various protein-protein interactions, and that SS18L1 may act as a fusion partner of SSX in synovial sarcoma. In the current study, we performed a comprehensive comparison of SNH-containing loci in several distinct species. By doing so, we found that the vertebrate SS18 and SS18L1 genes map within co-linear DNA segments that may have evolved through a relatively recent genomic duplication event. An additional phylogenetic study indicated that the more divergent SS18L2 gene is most likely derived from an earlier gene duplication event, again in the vertebrate lineage. Copyright © 2006 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

We have previously isolated and characterized a mouse cDNA orthologous to the human synovial sarcoma asso- ciated SS18 (formerly named SSXT and SYT)cDNA.Here,we report the characterization of the genomic structure of the mouse Ss18 gene.Through in silico methods with sequence information contained in the public databases,we did the same for the human SS18 gene and two human SS18 homologous genes,SS18L1 and SS18L2.In addition,we identified a mouse Ss18 processed pseudogene and mapped it to chromosome 1, band A2-3.The mouse Ss18 gene,which is subject to extensive alternative splicing,is made up of 11 exons,spread out over approximately 45 kb of genomic sequence.The human SS18 gene is also composed of 11 exons with similar intron-exon boundaries,spreading out over about 70 kb of genomic se- quence.One alternatively spliced exon,which is not included in the published SS18 cDNA,corresponds to a stretch of sequence which we previously identified in the mouse Ss18 cDNA.The human SS18L1 gene,which is also made up of 11 exons with similar intron-exon boundaries,was mapped to chromosome 20 band q13.3.The smaller SS18L2 gene,which is composed of three exons with similar boundaries as the first three exons of the other three genes,was mapped to chromosome 3 band p21. Through sequence and mutation analyses this gene could be excluded as a candidate gene for 3p21-associated renal cell can- cer.In addition,we created a detailed BAC map around the human SS18 gene,placing it unequivocally between the CA- repeat marker AFMc014wf9 and the dihydrofolate reductase pseudogene DHFRP1.The next gene in this map,located distal to SS18,was found to be the TBP associated factor TAFII-105 (TAF2C2).Further analogies between the mouse Ss18 gene,the human SS18 gene and its two homologous genes were found in the putative promoter fragments.All four promoters resemble the promoters of housekeeping genes in that they are TATA-less and embedded in canonical CpG islands [ABSTRACT FROM AUTHOR]