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Finding the position of a gene is now easily done when the genome sequence is available: the gene position is generally found by a simple query of genomic databases such as those available at the Ensembl browser or the NCBI. We were interested in determining the position of 125 cancer-related rat genes and we found that the position of most of these genes (110) could indeed be identified in this manner. However, in 15 cases, the gene position was not available in these databases, or the results were ambiguous. We then explored a more specialized database, namely the Rat Genome Database, and experimentally mapped these genes using standard and radiation cell hybrids. The 15 genes in question could be localized unambiguously. In four cases, the radiation cell hybrids were indispensable: the sequence of these four genes could not be found in the rat genome sequence. On the basis of the sample we examined, it thus appears that a classical gene mapping method is still required to localize about 3% of the rat genes, as if 3% of the rat gene sequences were lacking in the current rat genome sequence.

Identification and localization of genes that encode regulators of transcription could provide landmarks for functional analysis of the human genome. Toward this goal, we examined a panel of somatic cell hybrids and assigned the gene (TCF12) encoding the helix-loop-helix transcription factors 4 (HTF4) to chromosome 15. Fluorescence in situ hybridization further localized TCF12 to chromosome 15q21. Northern analysis revealed that the relative abundance of HTF4 gene transcripts is not constant but varies depending on the human cell-line or tissue examined.

Using fluorescence in situ hybridization, we determined the regional localization of the 3 rat genes encoding angiotensin II receptors at 17q12 (Agtr1a), 2q24 (Agtr1b) and Xq34 (Agtr2). In parallel, we showed that the type 2 human gene, AGTR2, also maps on the X chromosome, at band Xq22.

Through the use of somatic cell hybrids segregating either human or rat chromosomes, we determined the chromosome localizations of two genes encoding cAMP-specific phosphodiesterases (cAMP-PDEs). PDE4D, the gene encoding the cAMP-PDE isoform 3 (IVd), was assigned to human chromosome 5 and rat chromosome 2, and PDE4B, the gene encoding the cAMP-PDE isoform 4 (IVb), was assigned to human chromosome 1 and rat chromosome 5. These localizations extend the homology between rat chromosome 2 and human chromosome 5, on the one hand, and between rat chromosome 5 and human chromosome 1 on the other hand.

The Rfp (ret finger protein) and Olf89 (olfactory receptor 89) genes were assigned to rat chromosomes 17 and 20, respectively. These two genes are syntenic in human (RFP and OLF89) as they both map to chromosome 6, less than 300 kb apart. The mouse homologs are located on two different chromosomes, namely 13 and 17, respectively. It was shown that these two genes delineate the UA/UB break point, and that this chromosome break occurred in the rodent lineage, before the mouse radiation. Our data indicate that this break occurred before the rat/ mouse split, therefore before the Murinae radiation.

Comparative mapping between the rat and mouse genomes has shown that some chromosomes are entirely or almost entirely conserved with respect to gene content. Such is the case of rat chromosome 11 (RNO11) and mouse chromosome 16 (MMU16). We determined to what extent such an extensive conservation of synteny is associated with a conserved gene order. Therefore, we regionally localized several genes on RNO11. The comparison of the gene map of RNO11 and MMU16 unambiguously shows that the gene order has not been conserved in the Murinae lineage, thereby implying the occurrence of intrachromosomal evolutionary rearrangements. The transition from one chromosome configuration to the other one can be explained either by two intrachromosomal recombinations or by a single intrachromosomal recombination accompanied by neocentromere emergence.

The gene coding for rat parathyroid hormone-like peptide (PTHLH) was previously assigned to rat chromosome 2 (Hendy et al., 1988). We reexamined this assignment. According to our results, the gene is on rat chromosome 4. Taking into account the known localizations of the KRAS2 (Kras-2) oncogene and the PTHLH gene, this assignment strongly suggests that a synteny group is conserved on rat chromosome 4, mouse chromosome 6, and human chromosome 12.