Use of NotI microarrays in analysis of epigenetic and structural changes in epithelial tumor genomes by the example of human chromosome 3

Molecular Biology

Volumn 43, Issue 2, 2009, Pages 313-320

  Pavlova, T V ^a,b   Kashuba, V I ^b,c   Muravenko, O V ^a   Yenamandra, S P ^b   Ivanova, T A ^b   Zabarovska, V I ^b   Rakhmanaliev, E R ^b   Petrenko, L A ^b   Pronina, I V ^a,d   Loginov, V I ^d   Yurkevich, O Y ^a   Kisselev, L L ^a   Zelenin, A V ^a   Zabarovsky, E R ^a  

^a ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

^b KAROLINSKA INSTITUTE   (Sweden)

^c INSTITUTE OF MOLECULAR BIOLOGY AND GENETICS   (Ukraine)

^d STATE RESEARCH INSTITUTE OF GENETICS AND SELECTION OF INDUSTRIAL MICROORGANISMS   (Russian Federation)

Author keywords

Cancer genomics; Hemizygous deletion; Homozygous deletion; Human chromosome 3; Methylation; Microarrays; NotI linking clones

Indexed keywords

EID: 65349136005     PISSN: 00268933     EISSN: 16083245     Source Type: Journal    
DOI: 10.1134/S0026893309020137     Document Type: Article

References (25)

1. V. Trevino F. Falciani H.A. Barrera-Saldaña 2007 DNA microarrays: A powerful genomic tool for biomedical and clinical research Mol. Med. 13 527 541 (Pubitemid 47585747)
2. A.I. Su J.B. Welsh L.M. Sapinoso S.G. Kern P. Dimitrov H. Lapp P.G. Schultz S.M. Powell C.A. Moskaluk H.F. Frierson Jr. G.M. Hampton 2001 Molecular classification of human carcinomas by use of gene expression signatures Cancer Res. 61 7388 7393 (Pubitemid 32995021)
3. P.F. Macgregor 2003 Gene expression in cancer: The application of microarrays Expert. Rev. Mol. Diagn. 3 185 200 (Pubitemid 36313751)
4. B. Sadikovic J. Andrews D.I. Rodenhiser 2007 DNA methylation analysis using CpG microarrays is impaired in benzopyrene exposed cells Toxicol. Appl. Pharmacol. 225 300 309 (Pubitemid 350166476)
5. R.M. Brena T.H. Huang C. Plass 2006 Quantitative assessment of DNA methylation: Potential applications for disease diagnosis, classification, and prognosis in clinical settings J. Mol. Med. 84 365 377 (Pubitemid 43673611)
6. D. Zhou W. Qiao L. Yang Z. Lu 2006 Bisulfite-modified target DNA array for aberrant methylation analysis Anal. Biochem. 351 26 35 (Pubitemid 43160067)
7. B. Sadikovic J. Andrews D. Carter J. Robinson D.I. Rodenhiser 2007 Genome-wide H3K9 histone acetylation profiles are altered in benz[a]pyrene treated MCF7 breast cancer cells J. Biol. Chem. 283 4051 4060
8. J.R. Pollack C.M. Perou A.A. Alizadeh M.B. Eisen A. Pergamenschikov C.F. Williams S.S. Jeffrey D. Botstein P.O. Brown 1999 Genome-wide analysis of DNA copy-number changes using cDNA microarrays Nature Genet. 23 41 46 (Pubitemid 29418785)
9. J. Li A. Protopopov F. Wang V. Senchenko V. Petushkov O. Vorontsova L. Petrenko V. Zabarovska O. Muravenko E. Braga L. Kisselev M.I. Lerman V. Kashuba G. Klein I. Ernberg C. Wahlestedt E.R. Zabarovsky 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
10. E.R. Zabarovsky F. Boldog T. Thompson D. Scanlon G. Winberg Z. Marcsek R. Erlandsson E.J. Stanbridge G. Klein J. Sümegi 1990 Construction of a human chromosome 3 specific NotI linking library using a novel cloning procedure Nucl. Acids Res. 18 6319 6324 (Pubitemid 20379181)
11. V.I. Kashuba R.Z. Gizatullin A.I. Protopopov J. Li N.V. Vorobieva L. Fedorova V.I. Zabarovska O.V. Muravenko M. Kost-Alimova D.A. Domninsky C. Kiss R. Allikmets V.M. Zakharyev E.A. Braga J. Sumegi M. Lerman C. Wahlestedt A.V. Zelenin D. Sheer G. Winberg A. Grafodatsky L.L. Kisselev G. Klein E.R. Zabarovsky 1999 Analysis of NotI linking clones isolated from human chromosome 3 specific libraries Gene. 239 259 271 (Pubitemid 29512356)
12. S. Zöchbauer-Müller K.M. Fong A.K. Virmani J. Geradts A.F. Gazdar J.D. Minna 2001 Aberrant promoter methylation of multiple genes in non-small cell lung cancers Cancer Res. 61 249 255 (Pubitemid 32095725)
13. E.R. Zabarovsky M.I. Lerman J.D. Minna 2002 Tumor suppressor genes on chromosome 3p involved in the pathogenesis of lung and other cancers Oncogene 21 6915 6935 (Pubitemid 35221938)
14. J.G. Herman J.R. Graff S. Myohanen B.D. Nelkin S.B. Baylin 1996 Methylation-specific PCR: A novel PCR assay for methylation status of CpG islands Proc. Natl. Acad. Sci. USA. 93 9821 9826 (Pubitemid 26296693)
15. P.M. Warnecke C. Stirzaker J. Song C. Grunau J.R. Melki S.J. Clark 2002 Identification and resolution of artifacts in bisulfite sequencing Methods 27 101 107 (Pubitemid 34757119)
16. M. Toyota C. Ho N. Ahuja K.W. Jair Q. Li M. Ohe-Toyota S.B. Baylin J.P. Issa 1999 Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification Cancer Res. 59 2307 2312 (Pubitemid 29242273)
17. D.Y. Yoon P. Buchler S.T. Saarikoski O.J. Hines H.A. Reber O. Hankinson 2001 Identification of genes differentially induced by hypoxia in pancreatic cancer cells Biochem. Biophys. Res. Commun. 288 882 886 (Pubitemid 33140965)
18. Q. Feng A. Balasubramanian S.E. Hawes P. Toure P.S. Sow A. Dem B. Dembele C.W. Critchlow L. Xi H. Lu M.W. [tmp] McIntosh A.M. Young N.B. Kiviat 2005 Detection of hypermethylated genes in women with and without cervical neoplasia J. Natl. Cancer. 97 273 278 (Pubitemid 40310275)
19. T. Kuroki F. Trapasso S. Yendamuri A. Matsuyama H. Alder M. Mori C.M. Croce 2003 Allele loss and promoter hypermethylation of VHL, RAR-beta, RASSF1A, and FHIT tumor suppressor genes on chromosome 3p in esophageal squamous cell carcinoma Cancer Res. 63 3724 3728 (Pubitemid 36793058)
20. Q. Wang C. Yang J. Zhou X. Wang M. Wu Z. Liu 2001 Cloning and characterization of full-length human ribosomal protein L15 cDNA which was overexpressed in esophageal cancer Gene. 263 205 209 (Pubitemid 32167070)
21. V.I. Kashuba J. Li F. Wang V.N. Senchenko A. Protopopov A. Malyukova A.S. Kutsenko E. Kadyrova V.I. Zabarovska O.V. Muravenko A.V. Zelenin L.L. Kisselev I. Kuzmin J.D. Minna G. Winberg I. Ernberg E. Braga M.I. Lerman G. Klein E.R. Zabarovsky 2004 RBSP3 (HYA22) is a tumor suppressor gene implicated in major epithelial malignancies Proc. Natl. Acad. Sci. USA. 101 4906 4911 (Pubitemid 38469176)
22. K. Hibi K. Yamakawa R. Ueda Y. Horio Y. Murata M. Tamari K. Uchida T. Takahashi Y. Nakamura T. Takahashi 1994 Aberrant upregulation of a novel integrin alpha subunit gene at 3p21.3 in small cell lung cancer Oncogene 9 611 619 (Pubitemid 24041541)
23. J.L. Li Q. Fei J. Yu H.Y. Zhang P. Wang J.D. Zhu 2004 Correlation between methylation profile of promoter CpG islands of seven metastasis-associated genes and their expression states in six cell lines of liver origin Ai Zheng 23 985 991
24. V.N. Senchenko J. Liu W. Loginov I. Bazov D. Angeloni Y. Seryogin V. Ermilova T. Kazubskaya R. Garkavtseva V.I. Zabarovska V.I. Kashuba L.L. Kisselev J.D. Minna M.I. Lerman G. Klein E.A. Braga E.R. Zabarovsky 2004 Discovery of frequent homozygous deletions in chromosome 3p21.3 LUCA and AP20 regions in renal, lung and breast carcinomas Oncogene 23 5719 5728 (Pubitemid 39093017)
25. J.W. Gray C. Collins 2000 Genome changes and gene expression in human solid tumors. 2000 Carcinogenesis 21 443 452 (Pubitemid 30137929)