Construction of gene map of human chromosome 3 using RH-mapping of NotI-STSs

Rakhmanaliev, E.R.; Alexey, K.; Kompaniytsev, A.A.; Klimov, E.A.; Moisjak, E.V.; Udina, I.G.; Sulimova, G.E.

Авторы: Rakhmanaliev Elian R., Alexey Kutsenko, Kompaniytsev Alexey A., Klimov Eugene A., Moisjak Elena V., Udina Irina G., Sulimova Galina E.
Сборник: International Conference “Genomics, Proteomics and Bioinformatics for Medicine” (GPBM 2002). Abstract book
Тезисы
Год издания: 2002
Место издания: Moscow
Первая страница: 27
Последняя страница: 27
DOI: 10.13140/RG.2.1.4492.1845
Аннотация: The endonuclease NotI restriction sites (5'-GCGGCCGC-3') are located in CpG-island, which are associated with 5'-UTR of genes. Therefore STSs (sequenced tagged site), generated to the sequences around NotI-sites, might be considered as the universal markers of genes. Libraries of NotI-clones of human chromosomes 3 were constructed earlier. In our laboratory, 113 NotI-STSs for 84 NotI-clones were created. We have determined the physical localizations of 30 NotI-STSs by PCR screening of radiation hybrid panel GeneBridge4 and constructed the physical NotI-map of human chromosome 3, including 60 NotI-STSs. A BLAST homology search was performed for the localized NotI-clone genomic sequences against the public databases (GenBank, dbEST, EMBL, TIGR and “Draft Human Genome Database”). Significant homologies with known human genes and/or ESTs were shown for 91,7% NotI-clones. Therefore NotI-map is the gene map of human chromosome 3. The localization of the majority NotI-STSs and corresponding homologous genes and ESTs completely coincided. The application of the NotI-STSs as gene markers allowed detecting physical localizations of eight new nucleotide sequences on human chromosome 3, which have homology with genes, earlier localized on other human chromosomes. We have shown that RINZF gene earlier localized on 8q13-q21.1 has the full-length copy on human chromosome 3. Three genes (LOC132160, ATP11B and ITGA9) on chromosome 3, which markers by NotI-STSs, have similarity regulatory regions with the genes KIAA1157 (12q14.1), HSA9947 (1p36) and SCYA5 (17q11.2-q12), respectively. Similarity of functions for three pairs of the genes, (LOC132160 / KIAA1157, ATP11B / HSA9947 and ITGA9 / SCYA5), marked by the NotI-STSs, was shown. This allowed us to consider NotI-STSs as universal gene markers and apply them for the search and localization of new human genes, homologous genes and pseudogenes.
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