NotI Sequence-Tagged Sites as Markers of Genes on Human Chromosome 3
- 28 Downloads
- 3 Citations
Abstract
Using nucleotide sequences from jumping and linking NotI libraries of human chromosome 3, 94 NotI-STS markers for 72 individual NotI clones were developed. The positions of the NotI-STS markers and their order on the chromosome were determined by a combination of RH-mapping (our data), contig mapping, cytogenetic mapping, and in silico mapping. Comparison of NotI-STS DNAs with human genome sequences revealed two gaps in the regions 3p21.33 (marker NL1-256) and 3p21.31 (NL3-005), and a segmental duplication. Identical DNA fragments were found in the regions 12q and 3p22–21.33 (marker NL3-007). In the 3q28–q29 region (marker NLM-084), a fragment was detected whose identical copies were also present on chromosomes 1, 2, 15, and 19. For 69 NotI-STSs, significant homologies to nucleotide sequences of 70 genes and 2 cDNAs were detected (with homologies in NotI-STS 5′- and 3′-terminal sequences being taken into account). An association between NotI-STSs and genes is confirmed by a strong correlation between the density distributions of genes and NotI-STS markers on the map of human chromosome 3. Our results indicate that the NotI map may be regarded as a gene map of human chromosome 3. Thus, NotI-STSs are applicable as gene markers.
Key words
human chromosome 3 NotI clones NotI-STS markers PCR RH mapping physical mapping similarity to genes genomicsPreview
Unable to display preview. Download preview PDF.
REFERENCES
- 1.International Human Genome Sequencing Consortium. 2004. Finishing the euchromatic sequence of the human genome. Nature. 431, 931–945.Google Scholar
- 2.Eichler E.E., Clark R.A., She X. 2004. An assessment of the sequence gaps: Unfinished business in a finished human genome. Nature Rev. Genet. 5, 345–354.Google Scholar
- 3.Larsen F., Gundersen G., Lopez R., Prydz H. 1992. CpG islands as gene markers in the human genome. Genomics. 13, 1095–1107.CrossRefPubMedGoogle Scholar
- 4.Allikmets R.L., Kashuba V.I., Pettersson B., Gizatullin R., Lebedeva T., Kholodnyuk I.D., Bannikov V.M., Petrov N., Zakharyev V.M., Winberg G. 1994. NotI linking clones as a tool for joining physical and genetic mapping of the human genome. Genomics. 19, 303–309.CrossRefPubMedGoogle Scholar
- 5.Protopopov A.I., Gizatullin R.Z., Vorobieva N.V., Protopopova M.V., Kiss C., Kashuba V.I., Klein G., Kisselev L.L., Graphodatsky A.S., Zabarovsky E.R. 1996. High resolution FISH mapping of 50 NotI linking clones homologous to genes and cDNAs on human chromosome 3. Chromosome Res. 4, 443–447.PubMedGoogle Scholar
- 6.Bird A.P. 1987. CpG islands as gene markers in the vertebrate nucleus. Trends Genet. 3, 342–347.CrossRefGoogle Scholar
- 7.Sulimova G.E., Kutsenko A.S., Rakhmanaliev E.R., Udina I.G., Kompaniytsev A.A., Protopopov A.I., Moisjak E.V., Klimov E.A., Muravenko O.V., Zelenin A.V., Braga E.A., Kashuba V.I., Zabarovsky E.R., Kisselev L.L. 2002. Human chromosome 3: Integration of 60 NotI clones into a physical and gene map. Cytogenet. Genome. Res. 98, 177–183.CrossRefPubMedGoogle Scholar
- 8.Sulimova G.E., Udina I.G., Kunizheva S.S., Kompaniytsev A.A. 1999. Creating NitI-SOS markers of human chromosome 3. Mol. Biol. 33, 791–796.Google Scholar
- 9.Kashuba V.I., Gizatullin R.Z., Protopopov A.I., Li J., Vorobieva N.V., Fedorova L., Zabarovska V.I., Muravenko O.V., Kost-Alimova M., Domninsky D.A., Kiss C., Allikmets R., Zakharyev V.M., Braga E.A., Sumegi J., Lerman M., Wahlestedt C., Zelenin A.V., Sheer D., Winberg G., Grafodatsky A., Kisselev L.L., Klein G., Zabarovsky E.R. 1999. Analysis of NotI linking clones isolated from human chromosome 3 specific libraries. Gene. 239, 259–271.CrossRefPubMedGoogle Scholar
- 10.Protopopov A., Kashuba V., Zabarovska V.I., Muravenko O.V., Lerman M.I., Klein G., Zabarovsky E.R. 2003. An integrated physical and gene map of the 3.5-Mb chromosome 3p21.3 (AP20) region implicated in major human epithelial malignancies. Cancer Res. 63, 404–412.Google Scholar
- 11.Kashuba V.I., Szeles A., Allikmets R., Nilsson A.S., Bergerheim U.S., Modi W., Grafodatsky A., Dean M., Stanbridge E.J., Winberg G. 1995. A contig of NotI jumping and linking clones cover 2.5 MB in 3p21–p22 region suspected to contain tumor suppressor gene. Cancer. Genet. Cytogenet. 81, 144–150.Google Scholar
- 12.Sulimova G.E., Kompaniytsev A.A., Moisyak E.V., Rakhmanaliev E.R., Klimov E.A., Udina I.G., Zakharov I.A. 2000. Radiation mapping as a tool for making high-resolution physical maps of human and animal genomes. Radiat. Biol. Radioekol. 40, 520–528.Google Scholar
- 13.Kutsenko A.S., Gizatullin R.Z., Al-Amin A.N., Wang F., Kvasha S.M., Podowski R.M., Matushkin Y.G., Gyanchandani A., Muravenko O.V., Levitsky V.G., Kolchanov N.A., Protopopov A.I., Kashuba V.I., Kisselev L.L., Wasserman W., Wahlestedt C., Zabarovsky E.R. 2002. NotI flanking sequences: A tool for gene discovery and verification of the human genome. Nucleic Acids Res. 30, 3163–3170CrossRefPubMedGoogle Scholar
- 14.Zabarovsky E.R., Allikmets R., Kholodnyuk I., Zabarovska V.I., Paulsson N., Bannikov V.M., Kashuba V.I., Dean M., Kisselev L.L., Klein G. 1994. Construction of representative NotI linking libraries specific for the total human genome and for human chromosome 3. Genomics. 20, 312–316.CrossRefPubMedGoogle Scholar
- 15.Zabarovsky E.R., Kashuba V.I., Pettersson B., Petrov N., Zakharyev V., Gizatullin R., Lebedeva T., Bannikov V., Pokrovskaya E.S., Zabarovska V.I. 1994. Shotgun sequencing strategy for long-range genome mapping: A pilot study. Genomics. 21, 495–500.CrossRefPubMedGoogle Scholar
- 16.Sambrook J., Fritsch E.F., Maniatis T. 1989. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, N.Y.: Cold Spring Harbor Lab. Press.Google Scholar
- 17.Rakhmanaliev E.R., Klimov E.A., Sulimova G.E. 2004. Methods of mammalian genome mapping. Usp. Sovrem. Biol. 124, 286–302.Google Scholar
- 18.Olivier M., Aggarwal A., Allen J., Almendras A.A., Bajorek E.S., Beasley E.M., Brady S.D., Bushard J.M., Bustos V.I., Chu A., Chung T.R., De Witte A., Denys M.E., Dominguez R., Fang N.Y., Foster B.D., Freudenberg R.W., Hadley D., Hamilton L.R., Jeffrey T.J., Kelly L., Lazzeroni L., Levy M.R., Lewis S.C., Liu X., Lopez F.J., Louie B., Marquis J.P., Martinez R.A., Matsuura M.K., Misherghi N.S., Norton J.A., Olshen A., Perkins S.M., Perou A.J., Piercy C., Piercy M., Qin F., Reif T., Sheppard K., Shokoohi V., Smick G.A., Sun W.L., Stewart E.A., Fernando J., Tejeda Tran N.M., Trejo T., Vo N.T., Yan S.C., Zierten D.L., Zhao S., Sachidanandam R., Trask B.J., Myers R.M., Cox D.R. 2001. A high-resolution radiation hybrid map of the human genome draft sequence. Science. 291, 1298–1302.Google Scholar
- 19.Caron H., van Schaik B., van der Mee M., Baas F., Riggins G., van Sluis P., Hermus M.C., van Asperen R., Boon K., Voute P.A., Heisterkamp S., van Kampen A., Versteeg R. 2001. The human transcriptome map: Clustering of highly expressed genes in chromosomal domains. Science. 291, 1289–1292.CrossRefPubMedGoogle Scholar
- 20.Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., Holt R.A., Gocayne J.D., Amanatides P., Ballew R.M., Huson D.H., Wortman J.R., Zhang Q., Kodira C.D., Zheng X.H., Chen L., Skupski M., Subramanian G., Thomas P.D., Zhang J., Gabor Miklos G.L., Nelson C., Broder S., Clark A.G., Nadeau J., McKusick V.A., Zinder N., Levine A.J., Roberts R.J., Simon M., Slayman C., Hunkapiller M., Bolanos R., Delcher A., Dew I., Fasulo D., Flanigan M., Florea L., Halpern A., Hannenhalli S., Kravitz S., Levy S., Mobarry C., Reinert K., Remington K., Abu-Threideh J., Beasley E., Biddick K., Bonazzi V., Brandon R., Cargill M., Chandramouliswaran I., Charlab R., Chaturvedi K., Deng Z., Di Francesco V., Dunn P., Eilbeck K., Evangelista C., Gabrielian A.E., Gan W., Ge W., Gong F., Gu Z., Guan P., Heiman T.J., Higgins M.E., Ji R.R., Ke Z., Ketchum K.A., Lai Z., Lei Y., Li Z., Li J., Liang Y., Lin X., Lu F., Merkulov G.V., Milshina N., Moore H.M., Naik A.K., Narayan V.A., Neelam B., Nusskern D., Rusch D.B., Salzberg S., Shao W., Shue B., Sun J., Wang Z., Wang A., Wang X., Wang J., Wei M., Wides R., Xiao C., Yan C., Yao A., Ye J., Zhan M., Zhang W., Zhang H., Zhao Q., Zheng L., Zhong F., Zhong W., Zhu S., Zhao S., Gilbert D., Baumhueter S., Spier G., Carter C., Cravchik A., Woodage T., Ali F., An H., Awe A., Baldwin D., Baden H., Barnstead M., Barrow I., Beeson K., Busam D., Carver A., Center A., Cheng M.L., Curry L., Danaher S., Davenport L., Desilets R., Dietz S., Dodson K., Doup L., Ferriera S., Garg N., Gluecksmann A., Hart B., Haynes J., Haynes C., Heiner C., Hladun S., Hostin D., Houck J., Howland T., Ibegwam C., Johnson J., Kalush F., Kline L., Koduru S., Love A., Mann F., May D., McCawley S., McIntosh T., McMullen I., Moy M., Moy L., Murphy B., Nelson K., Pfannkoch C., Pratts E., Puri V., Qureshi H., Reardon M., Rodriguez R., Rogers Y.H., Romblad D., Ruhfel B., Scott R., Sitter C., Smallwood M., Stewart E., Strong R., Suh E., Thomas R., Tint N.N., Tse S., Vech C., Wang G., Wetter J., Williams S., Williams M., Windsor S., Winn-Deen E., Wolfe K., Zaveri J., Zaveri K., Abril J.F., Guigo R., Campbell M.J., Sjolander K.V., Karlak B., Kejariwal A., Mi H., Lazareva B., Hatton T., Narechania A., Diemer K., Muruganujan A., Guo N., Sato S., Bafna V., Istrail S., Lippert R., Schwartz R., Walenz B., Yooseph S., Allen D., Basu A., Baxendale J., Blick L., Caminha M., Carnes-Stine J., Caulk P., Chiang Y.H., Coyne M., Dahlke C., Mays A., Dombroski M., Donnelly M., Ely D., Esparham S., Fosler C., Gire H., Glanowski S., Glasser K., Glodek A., Gorokhov M., Graham K., Gropman B., Harris M., Heil J., Henderson S., Hoover J., Jennings D., Jordan C., Jordan J., Kasha J., Kagan L., Kraft C., Levitsky A., Lewis M., Liu X., Lopez J., Ma D., Majoros W., McDaniel J., Murphy S., Newman M., Nguyen T., Nguyen N., Nodell M., Pan S., Peck J., Peterson M., Rowe W., Sanders R., Scott J., Simpson M., Smith T., Sprague A., Stockwell T., Turner R., Venter E., Wang M., Wen M., Wu D., Wu M., Xia A., Zandieh A., Zhu X. 2001. The sequence of the human genome. Science. 291, 1304–1351.CrossRefPubMedGoogle Scholar
- 21.Yang Q., Yoshimura G., Mori I., Sakurai T., Kakudo K. 2002. Chromosome 3p and breast cancer. J. Hum. Genet. 47, 453–459.CrossRefPubMedGoogle Scholar
- 22.Braga E.A., Kisselev L.L., Zabarovsky E.R. 2004. From identification of genomic polymorphism to diagnostic and prognostic markers of human epithelial tumors. Mol. Biol. 38, 179–190.CrossRefGoogle Scholar
- 23.Chakraborty S.B., Dasgupta S., Roy A., Sengupta A., Ray B., Roychoudhury S., Panda C.K. 2003. Differential deletions in 3p are associated with the development of head and neck squamous cell carcinoma in Indian patients. Cancer Genet. Cytogenet. 146, 130–138.CrossRefPubMedGoogle Scholar
- 24.Zabarovsky E.R., Petrenko L., Protopopov A., Vorontsova O., Kutsenko A.S., Zhao Y., Kilosanidze G., Zabarovska V., Rakhmanaliev E., Pettersson B., Kashuba V.I., Ljungqvist O., Norin E., Midtvedt T., Mollby R., Winberg G., Ernberg I. 2003. Restriction site tagged (RST) microarrays: A novel technique to study the species composition of complex microbial systems. Nucleic Acids Res. 15, e95.CrossRefGoogle Scholar
- 25.Li J., Protopopov A., Wang F., Senchenko V., Petushkov V., Vorontsova O., Petrenko L., Zabarovska V., Muravenko O., Braga E., Kisselev L., Lerman M.I., Kashuba V., Klein G., Ernberg I., Wahlestedt C., Zabarovsky E.R. 2002. NotI subtraction and NotI-specific microarrays to detect copy number and methylation changes in whole genomes. Proc. Natl. Acad. Sci. USA. 99, 10724–10729.CrossRefPubMedGoogle Scholar