Gen Anlatımı Analiz Yöntemlerine Genel Bakış

Abstract

Çeşitli doku veya hücre serilerinde gözlenen biyolojik ve fizyopatolojik durumlar gen anlatımındaki kalitatif ve kantitatif farklılıklardan kaynaklanmaktadır. Karşılaştırmalı gen anlatım analizinde kullanılan çeşitli yaklaşımlar ve teknikler mevcuttur. Bu yöntemler dizileme temelli, PZR temelli, hibridizasyon temelli ve kombine yöntemler olarak sınıflandırılabilinir. Çıkartılmış hibridizasyon kütüphanesi yöntemi, araştırılan doku veya hücre hatlarında farklı olarak ifade edilen genlerin belirlenmesi ve izolasyonunda uygulanan güçlü yaklaşımlardan birisidir. Son dönemdeki teknolojik gelişmelere göre büyük ölçekli gen ifade analizleri ile çok sayıda genin biyolojik ve patolojik olaylardaki transkripsiyonel yanıtları hızlı olarak araştırılabilmektedir. Ancak, her tekniğin uygulamalarında çeşitli üstünlükler veya sınırlılıklar mevcuttur. Sonuç olarak bu makalenin konusu, çıkartılmış hibridization kütüphanesi ve diğer gen ekspresyon analizi yöntemlerinin birbirleri ile karşılaştırmasıdır.

References

1. Stanton LW. Methods to profile gene expression. Trends Cardiovascular Medicine 2001; 11: 49-54.
2. Hess J, Laumen H, Wirth T. Application of differential cDNA screening techniques to the identification of unique gene expression in tumours and lymphocytes. Current Opinion in Immunology 1998; 10:125-130.
3. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF, ve ark. Complemantary DNA sequencing: expressed sequence tags and human genome project. Science 1991; 252: 1651-1656.
4. Kodzius R, Matsumura Y, Kasukawa T, Shimokawa K, Fukuda S, Shiraki T, Nakamura M, Arakawa T, Sasaki D, Kawai J, Harbers M, Carninci P, Hayashizaki Y. Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags. FEBS Letters 2004; 559, 22-6.
5. Hill DP, Begley DA, Finger JH, Hayamizu TF, McCright U, Smith CM, Beal JS, Corbani LE, Blake JA, Eppig JT, Kadin JA, Richardson JE, Ringwald M. The mouse Gene Expression Database (GXD): updates and enhancements. Nucleic Acids Research 2004; 32, D568-71.
6. Hwang DM, Dempsey AA, Lee C, Liew C. Identification of differentially expressed genes in cardiac hypertrophy by analysis of expressed sequence tags. Genomics 2000; 66,1-14.
7. Tabibiazar R, Wagner RA, Liao A, Quertermous T. Transcriptional profiling of the heart reveals chamber-specific gene expression patterns. Circulation Resarch 2003; 93: 1193¬ 201.
8. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. Serial analysis of gene expression. Science 1995; 270: 484¬ 487.

9. Ye SQ, Lavoie T, Cusher D, Zhang LQ. Microarray, SAGE and their applications to cardivascular disease. Cell Research 2002; 12: 105-115.
10. Reinartz J, Bruyns E, Lin JZ, Burcham T, Brenner S, Bowen B, Kramer M, Woychik R. Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms. Brief Funct Genomic Proteomic. 2002; 1: 95-104.
11. Meyers BC, Tej SS, Vu TH, Haudenschild CD, Agrawal V, Edberg SB, Ghazal H, Decola S. The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. Genome Res. 2004; 14 :1641-53.
12. Higuchi R, Fodder C, Dollinger G, Watson R. Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Biotechnology 1993; 11: 1026.
13. Kubista M, Andrade JM, Bengtsson M, Forootan A, Jonâk J, Lind K, Sindelka R, Sjöback R, Sjögreen B, Strömbom L, Stâhlberg A, Zoric N. The real-time polymerase chain reaction. Molecular Aspects Medicine 2006; 27: 95-125.
14. Ginzinger DG. Gene quantification using real-time quantitative PCR: An emerging technology hits the mainstream. Experimental Hematology 2002; 30: 503-512.
15. Klein D. Quantification using real-time PCR technology: applications and limitations. Trends in Molecular Medicine 2002; 8: 257-260.
16. Liang P, Pardee AB. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 1992; 257: 967-971.
17. Khare S, Kumar U, Sasi R, Puebla L, Calderon L, Lemstrom K, Hayry P, Patel AY. Differential regulation of somatostatin receptor types 1-5 in rat aorta after angioplasty. The FASEB Journal 1999; 13: 387-394.
18. Yang D, Yu J, Luo Z, Carthy CM, Wilson JE, Liu Z, McManus BM. Viral myocarditis: identification of five differentially expressed genes in coxsackievirus B3-infected mouse heart. Circulation Research 1999; 84: 704-712.
19. Tyagi SC, Kumar S, Voelker DJ, Reddy HK, Janicki JS, Curtis JJ. Differential gene expression of extracellular matrix components in dilated cardiomyopathy. Journal of Cellular Biochemistry 1996; 63: 185-98.
20. Pak BJ, Pang SC. Developmental regulation of the translational repressor NAT1 during cardiac development. Journal of Molecular and Cellular Cardiology 1999; 31:1717¬ 1724.
21. Kessler C. Nonradioactive analysis of biomolecules. (). Berlin, Heidelberg, New York: Springer Verlag, 2nd ed., 2000.
22. Schulze A, Downward J. Navigating gene expression using microarrays- a technology review. Nature Cell Biology 2001;3:E190-E195.
23. Medeiros F, Rigl CT, Anderson GG, Becker SH, Hailing KC. Tissue handling for genome-wide expression analysis: a review of the issues, evidence, and opportunities. Archives of Pathology and Laboratory Medicine 2007; 131. 1805-1816.
24. Nanni L, Romualdi C, Maşeri A, Lanfranchi G. Differential gene expression profilling in genetic and multifactorial cardiovascular disease. Journal of Molecular and Cellular Cardiology 2006; 41: 934-948.
25. Sambrook J, Russell DW. Molecular Cloning a Laboratory Manual. New York: Cold Spring Harbor Laboratory Press, 3rd ed., 2001.
26. Alwine JC, Kemp DJ, Stark GR. Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proceedings of the National Academy of Sciences of the United States of America 1977; 74: 5350-4.
27. Kozian DH, Kirschbaum BJ. Comparative geneexpression analysis. Trends in Biotechnology 1999; 17: 73¬ 78.
28. Jin L, Lloyd RV. In situ hybridization: methods and applications. Journal of Clinical Laboratory Analysis 1997; 11: 2-9.
29. Wilcox JN. In situ hybridization, DVA-Concepts in molecular medicine, Course outline. Emory University, 1996. Eri§im 05.09.2008, http://www.emory.eduAVILCOX/DVApartl.html.
30. Kononen J, Bubendorf L, KalUoniemi A, Barlund M, Schraml P, Leighton S, Torhorst, J, Mihatsch MJ, Sauter G, Kallioniemi OP. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nature Medicine 1998; 4: 844-847.
31. Kumar B, de Silva M, Venter DJ, Armes JE. Tissue microarray: a practical guide. Pathology 2004; 36; 295-300.
32. Henshall S. Tissue Microarray. Journal of Mammary Gland Biology and Neoplasia 2003; 8: 347-358.
33. Hubark M, Schatz DG. Identifying differences in mRNA expression by representational difference analysis of cDNA. Nucleic Acids Res 1994; 22: 5640-5648.
34. Suzuki Y, Sato N, Tohyama M, Wanaka A, Takagi T. Efficient isolation of differentially expressed genes by means of a newly established method, 'ESD'. Nucleic Acids Res 1996; 24: 797-799.
35. Hara E, T. Kato E, Nakada S, Sekiya S, Oda K. Subtractive cDNA cloning using oligo(dT)30-latex and PCR: isolation of cDNA clones specific to undifferentiated human embryonal carcinoma cells. Nucleic Acids Res 1991; 19:7097¬ 7104.
36. Kuang WW, Thompson DA, Hoch RV, Weigel RJ. Differential screening and suppression subtractive hybridization identified genes differentially expressed in an estrogen recetorpositive breast carcinoma cell line. Nucleic Acids Res 1998; 26: 1116-1123.
37. Stubbs AP, Abel PD, Golding M, Bhangal G, Wang C, Waxman JU, Stamp GWH, Lalani E. Differentially exppressed genes in hormone refractory prostate cancer. Am J Pathol 1999; 154: 1335-1343.
38. Morozov G, Verlinsky O, Rechitsky S, Ivakhnenko V, Goltsman E, Gindilis V, Strom C, Kuliev A, Verlinsky Y. Contraction and analysis of subtraction complementary DNA libraries from human preimplantation embryos. J Ass Repr Genet 1999; 16: 212-215.
39. Wieland I , Bolger G, Asouline G, Wigler M. A method for difference cloning:Gene amplification following subtractive hybridization. Proc Natl Acad Sci USA 1990; 87: 2720-2724.
40. Lamar EE, Palmer E. Y-encoded, species-specific DNA in mice:evidence that the Y chromosome exists in two polymorphic forms in inbred strains. Cell 1984; 37: 171-177.
41. Winer J, Jung CKS, Shackel I , Williams PM. Development and validation of real-time quantitative reverse transcriptase-polymerase chain reaction for monitoring gene expression in cardiac myocytes in vitro. Anal Biochem 1999; 270: 41-49.
42. Timblin C, Battey J, Kuehl WM. Application for PCR technology to subtractive cDNA cloning: identification of genes expressed specifically in murine plasmacytoma cells. Nucleic Acids Res 1990; 18: 1587-1593.
43. Wieland I , Bolger G, Asouline G, Wigler M. A method for difference cloning:Gene amplification following subtractive hybridization. Proc Natl Acad Sci USA 1990; 87: 2720-2724.
44. Meszaros M, Morton DB. Subtractive hybridization strategy using paramagnetic oligo(dT) beads and PCR. BioTechniques 1996; 20: 413-419.
45. van Miltenburg, R., Rûger, B., Griinewald-Janho, S., Leons, M., Schroder, C. The DIG System User's Guide for Filter Hybridization. Germany: Boehringer Mannheim GmbH, Biochemica, 1995.
46. Diatchenko L, Lau YF, Campbell AP, Chenchik A, Moqadam F, Huang B, Lukyanov S, Lukyanov K, Gurskaya N, Sverdlov ED, Siebert PD. Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 1996; 93: 6025-6030.
47. von Stein OD, Thies WG, Hofmann M. A high throughput screening for rarely transcribed differentially expressed genes. Nucleic Acids Res 1997; 25: 2598-602.
48. Zhang H, Zhou L, Yang R, Sheng Y, Sun W, Kong X, Cao K. Identification of differentially expressed genes in human heart with ventricular septal defect using suppression subtractive hybridization. Biochem Biophys Res Commun. 2006; 342:135-44.
49. Liang G, Zhang XD, Wang LJ, Sha YS, Zhang JC, Miao SY, Zong SD, Wang LF, Koide SS. Identification of differentially expressed genes of primary spermatocyte against round spermatid isolated from human testis using the laser capture microdissection technique. Cell Res 2004; 14:507-12.
50. Rebrikov DV, Britanova OV, Gurskaya NG, Lukyanov KA, and Lukyanov SA. Mirror orientation selection (MOS) a method for ekminating false positive clones from libraries generated by suppression subtractive hybridization. Nucleic Acids Res 2000; 28:E90.
51. Medeiros F, Rigl CT, Anderson GG, Becker SH, Hailing KC. Tissue handling for genome-wide expression analysis: a review of the issues, evidence, and opportunities. Archives of Pathology and Laboratory Medicine 2007; 131: 1805-1816.
52. Ross JS, Ginburg GS. The integration of molecular diagnostics with therapeutics: implications for drug development and pathology practice. American Journal of Clinical Pathology 2003; 119: 26-36.