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Of Unusual Organization Dorothee F6rnzler, 1'3 Joachim Altschmied, 1'4 Indrajit Nanda, 2 Renate Kolb, Monika Baudler Michael Schmid, 2 and Manfred Schartl 1

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Of Unusual Organization Dorothee F6rnzler, 1'3 Joachim Altschmied, 1'4 Indrajit Nanda, 2 Renate Kolb, Monika Baudler Michael Schmid, 2 and Manfred Schartl 1 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press RESEARCH The Xmrk Oncogene Promoter is Derived from a Novel Amplified Locus of Unusual Organization Dorothee F6rnzler, 1'3 Joachim Altschmied, 1'4 Indrajit Nanda, 2 Renate Kolb, Monika Baudler Michael Schmid, 2 and Manfred Schartl 1 1Physiological Chemistry I, Theodor Boveri Institute for Biosciences (Biocenter), 2Department of Human Genetics, University of WLirzburg, 97074 W~irzburg, Germany Hereditary melanoma in Xiphophorus hybrids is caused by the receptor tyrosine kinase Xmrk. Tumor formation is initiated by overexpression of the Xmrk gene, apparently because of insufficient transcriptional control in the melanocytic lineage of hybrid fish. The oncogenic Xmrk resulted from gene duplication and nonhomologous recombination of the corresponding Xmrk proto-oncogene during evolution. By this event Xmrk was translocated downstream of the promoter of another gene, D (for Donor). This raised the question whether both the Xmrk oncogene and D share similar transcriptional control elements. Studies on the genomic organization of D showed that this gene is amplified in the Xiphophorus genome, presumably with all copies clustered on a single chromosome. Surprisingly, at least two completely different, tightly linked genes are included in the amplified segment. We find a ubiquitously expressed zinc finger gene of the kr@pel type, followed by a previously unknown gene, which was the partner of the Xmrk proto-oncogene in the recombination generating the Xmrk oncogene. The nucleotide sequence predicts a gene product with very high amino acid similarity to a hypothetical Caenorhabditis elegans protein. The expression pattern is unrelated to that of the Xmrk oncogene suggesting that despite extended sequence homology a new type of promoter was created by this rearrangement. In Xiphophorus fish certain hybrid genotypes RET convert the proto-oncogene into a dominant spontaneously develop malignant melanoma. transforming gene, which can be transmitted Responsible for this melanoma formation is the through the germ line (Santoro et al. 1995). Thus, receptor tyrosine kinase Xmrk (Wittbrodt et al. the Xiphophorus melanoma system might serve as 1989). Several cellular receptor tyrosine kinases a model for analyzing the mechanisms by which are known to play a role in human malignancies a deleterious gene is stably maintained in the ge- either after activation of the corresponding netic material and how germ-line transmission is proto-oncogenes by translocation, mutation, am- facilitated. In the Xiphophorus genome, the Xrnrk plification, and subsequent overexpression, or as gene is present in two different copies, both lo- transforming genes in the genomes of retrovi- cated on the sex chromosomes. All individuals of ruses. However, Xmrk was the first case, where it the genus investigated so far carry the proto- was shown that an activated oncogene is passed oncogenic version of the gene. However, the on- through the germ line without being harmful to cogenic Xmrk locus is only present in those fish, the organism. A comparable situation has been such as the platyfish Xiphophorus maculatus, that described recently in humans in multiple endo- exhibit specific pigmentation patterns marked by crine neoplasias type 2A and 2B and familial a peculiar cell type, the macromelanophores. Af- medullary thyroid carcinomas. Here, mutations ter crossing with another Xiphophorus species, in the gene for the receptor-like tyrosine kinase such as the swordtail Xiphophorus helleri, that has ZPresent address: Brigham k Women's Hospital, Harvard neither macromelanophores nor the Xmrk onco- Medical School, Boston, Massachusetts 02115. gene, benign and malignant melanoma originat- 4Corresponding author. E-MAIL [email protected]; FAX 49-931- ing from the macromelanophore spots appear in 8884150. the offspring generations. In the parental platy- 102 @GENOME RESEARCH 6:102-113 ©1996 by Cold Spring Harbor Laboratory Press ISSN 1054-9803/96 $5.00 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press UNUSUAL ORGANIZATION OF A GENE CLUSTER IN FISH fish, spontaneous melanoma formation generally We show here that D is not a single-copy does not occur, owing to the presence of a tumor gene in the Xiphophorus genome but is an ampli- suppressor locus R, thus far uncharacterized, that fied locus that is clustered on a single chromo- counteracts the oncogenic activation of Xmrk. some. In addition, the D locus contains at least This locus is unlinked to the Xmrk oncogene and two structurally unrelated genes, one that en- can segregate from it. This leads to benign mela- codes a zinc finger protein of the kriippel type, noma in progeny with one R locus still present, and one that contains an open reading frame and to malignant melanoma, when R is com- (ORF) identifying a novel putative protein, which pletely absent (for review of the Xiphophorus mel- in some domains is highly conserved throughout anoma system, see Altschmied and Schartl 1994). evolution. Both of their expression patterns do Although the nucleotide sequences of both not match that of the Xmrk oncogene. Xmrk copies are 99% identical (Adam et al. 1991), the expression patterns of the Xmrk proto- RESULTS oncogene and oncogene are completely differ- Amplification and Chromosomal Localization of ent. The proto-oncogene is expressed at low lev- the D Locus els in a number of nontumorous tissues and in melanomas, without any correlation with the se- In the initial experiments that identified the D verity of the phenotype. In contrast, the Xmrk locus, it appeared that this could be a multicopy oncogene is expressed exclusively in melanoma sequence (Adam et al. 1993). For a more detailed and its expression depends on the absence of analysis, genomic DNA from various Xiphophorus the tumor suppressor gene R. The expression genotypes and species was digested with different level correlates positively with the state of restriction enzymes and the size-fractionated malignancy. DNA was hybridized with a 0.3-kb fragment de- It has been shown that the Xmrk proto- rived from the Xmrk oncogene promoter region oncogene and oncogene differ in their 5'- that had been isolated previously and is identical promoter regions (Adam et al. 1993). This can be to D (Adam et al. 1993) and a 0.4-kb fragment explained by a gene duplication of the ancestral directly upstream. The results clearly show that Xmrk proto-oncogene. During the course of this the D locus contains an amplified gene. The frag- event the new Xmrk copy was translocated down- ments detected with the 0.3-kb probe seem to be stream of the promoter of a different gene locus located in a conserved core region of this ampli- D (D for Donor), resulting in the creation of the fied gene locus, therefore revealing only a few, oncogene. This suggested that in the wild-type but strongly hybridizing bands (Fig. 1A). In con- fish, which never develop melanoma, the D-de- trast, the upstream flanking region shows high rived oncogene promoter is transcriptionally intraspecific variability (Fig. 1B). Hybridization controlled, either directly or indirectly, by R. was also obtained with DNA from a different Elimination of the suppressor R following genetic strain of Xiphophorus maculatus, X. helleri, and the segregation can lead to overexpression of Xmrk X. xiphidium-derived embryonic epithelial cell and to melanoma formation. Thus, it appears line A2 (Kuhn et al. 1979), all of which do not that the tumor suppressor function of R is an ac- carry the Xmrk oncogene in their genome. This cidental side effect of the transcriptional regula- indicates that the presence of the D locus is not tion that R normally exerts on D (Schartl 1995). restricted to fish with a genetic predisposition to This hypothesis for D and the Xmrk onco- melanoma formation. In an analysis of 89 indi- gene raises the following questions: Are the pro- viduals from 8 purebred species and 21 interspe- moters still functionally equivalent, that is, do cific hybrids of various genotypes, we have not the genes have similar expression patterns? Or found a single genotype without a D locus. A did the gene duplication create a novel, unrelated rough estimate based on the number of bands transcriptional control region that directs a and signal strength in Figure 1B shows that the unique expression pattern to the oncogene, Xiphophorus genome contains ~20 copies of the D namely, exclusively in macromelanophores of locus. Similar results were obtained using a 0.6-kb hybrid fish? The knowledge of the structure of probe from the 3' end of the previously charac- the D-locus gene product and its expression terized 2.1-kb EcoRI D locus fragment (data not could give additional clues as to why the Xmrk shown). oncogene is out of proper transcriptional control To isolate D locus genomic sequences a X. in melanoma. maculatus library was screened at high stringency GENOME RESEARCH @ 103 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press FORNZLER ET AL. A B the transcription of these genes, we isolated pro- Eco RI Hinc II ECO RI moter fragments from X. maculatus genomic kb 1 2 3 1 2 3 4 kb 5 6 DNA using a PCR approach. This amplification yielded three different promoter sequences in ad- dition to the corresponding fragments from the 6.6-- 5.1-- four phages. All sequences are highly homolo- 4.3-- gous but clearly distinct (Fig. 4). In a parsimony 3.5 - analysis the evolutionary relationship between 2.3 ~ the different D gene promoters and the corre- sponding Xmrk oncogene sequences was estab- 1.6-- ! lished. Included in this analysis was the region between position -625 and -13 relative to the Figure 1 Amplification of the D locus. (A) Conser- Xmrk transcriptional start site; D1 was omitted, vation of the core region.
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