Genomik ve Proteomik
Özet
Canlılarda bulunan farklılıkların gen ve protein seviyesinde belirlenmesi, mutasyona ve/veya delesyona uğrayan nükleotitlerin tespiti, proteinlerin işlevinin/yapısının değerlendirilmesi ve bunların sebep olduğu etkilerin araştırılması hem hastalıkların tedavi sürecinde hem de tür içi ve türler arası varyasyon çalışmalarında oldukça önemlidir. Genler dışında genomda bulunan kodlamaya yapmayan bölgeler ve tekrar dizileri de sıklıkla varyasyon göstermektedir. Bu anlamda canlıların genom dizilemesinin yapılması ve yan yana gelen milyonlarca nükleotit dizisinin alfabe dilini çözerek canlının genom organizasyonunun aydınlatılması oldukça önemli ve yeni bir çalışma alanıdır. Proteomik yaklaşımında ise biyobelirteçlerin keşfi hala büyük bir heyecanla devam etmektedir. Proteomik çalışmalarının genomik ve biyoinformatik ile birleştirilmesi biyolojik sistem bilgilerinin ve hastalık modellerinin anlaşılmasını daha önemli kılmaktadır. Bu bölümde genom kavramı, genom haritaları, genom analizi yapılmış olan canlıların birbirleriyle kıyaslanması, proteom kavramı, proteomik tipleri ve şimdiye kadar insanlar ile ilgili genomik ve proteomik seviyede yapılan çalışmalardan bahsedilmiştir.
Referanslar
Pearson H. What is a gene?. Nature; 2006;441(7092):398-402.
Demongeot J, Seligmann H. Why is AUG the start codon? Theoretical minimal RNA rings: Maximizing coded information biases 1st codon for the universal initiation codon AUG. Bioessays; 2020; 42(6):1900201. doi: 10.1002/bies.202000061.
Hecht J, Glasgow PR, Jaschke LA, et al. Measurements of translation initiation from all 64 codons in E. coli. Nucleic acids research; 2017;45(7):3615-3626. doi: 10.1093/nar/gkx070.
Başaran E, Aras S, Cansaran-Duman D. Genomik, proteomik metabolomik kavramlarına genel bakış ve uygulama alanları. Türk Hijyen ve Besinsel Biyoloji Dergisi; 2010; 67:85-96.
Winkler H. Verbreitung und Ursache der Parthenogenesis im Pflanzen- und Tierreiche. Verlag Fischer; 1920, Jena.
Nadeau JH, Davisson MT, Doolittle DP, et al. Comparative map for mice and humans. Mammalian Genome; 1992; 3(9):480-536.
Sarwal M, Alemi F. Genomics and Microarray. In: Lotze M, Thomson A (eds.) Measuring Immunity Basic Science and Clinical Practise. Great Britain: Elsevier; 2005. p. 697-706.
Bal SH, Budak F. Genomik, proteomik kavramlarına genel bakış ve uygulama alanları. Uludağ Üniversitesi Tıp Fakültesi Dergisi; 2013; 39(1):65-69.
Fleischmann RD, Adams MD, White O, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science; 1995;269(5223):496-512. doi: 10.1126/science.7542800.
Goffeau A, Barrell BG, Bussey H, et al. Life with 6000 genes. Science; 1996;274:546–567. doi: 10.1126/science.274.5287.546.
The C. elegans Sequencing Consortium. Genome sequence of the nematode, C. elegans: A platform for investing biology. Science; 1998;282:2012–2018. doi: 10.1126/science.282.5396.2012.
Adams MD, Celniker SE, Holt RA, et al. The genome sequence of Drosophila melanogaster. Science; 2000; 287(5461): 2185-2195. doi: 10.1126/science.287.5461.2185.
Allocca M, Zola S, Bellosta P. The fruit fly, Drosophila melanogaster: the making of a model (Part I). In: Perveen FK, (eds.) Drosophila melanogaster: Model for Recent Advances in Genetics and Therapeutics. Rijeka, Croatia: InTech;2018. p.113- 130.
Pandey UB, Nichols CD. Human disease models in Drosophila melanogaster and the role of the fly in therapeutic drug discovery. Pharmacol Rev.; 2011;63:412-431. doi: 10.1124/pr.110.003293.
Baenas N, Wagner AE. Drosophila melanogaster as an alternative model organism in nutrigenomics. Genes Nutr. 2019;14:1-11. doi: 10.1186/s12263-019-0641-y.
Meinke DW, Cherry JM, Dean C, et al. Arabidopsis thaliana: a model plant for genome analysis. Science; 1998; 282(5389):662-682. doi: 10.1126/science.282.5389.662.
Goff SA, Ricke D, Lan TH, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science; 2002; 296(5565): 92-100. doi: 10.1126/science.1068275.
Karami A. Largest and smallest genome in the World; 2013.
Frith MC, Pheasant M, Mattick JS. The amazing complexity of the human transcriptome. European journal of human genetics: EJHG; 2005; 13(8):894-897. doi: 10.1038/sj.ejhg.5201459.
Ateş K. Gen mi, RNA mı?. Deneysel Tıp Araştırma Enstitüsü Dergisi; 6(11):43-49.
Fiers W, Contreras R, Duerinck F, et al. Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene. Nature; 1976; 260(5551):500-507. doi: 10.1038/260500a0.
Nurk S, Koren S, Rhie A, et al. The complete sequence of a human genome. Science; 2022; 376(6588):44-53. doi: 10.1126/science.abj6987.
International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature; 2007; 449(7164):851. doi: 10.1038/nature06258.
International HapMap Consortium. A haplotype map of the human genome. Nature; 2005; 437(7063):1299. doi: doi.org/10.1038/nature04226.
Gibbs RA, Belmont JW, Hardenbol P, et al. The international HapMap project. 2003. doi:10.1038/nature02168.
Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proceedings of the national academy of sciences; 1977; 74(12):5463-5467. doi: 10.1073/pnas.74.12.5463.
Adams JU. DNA Sequencing Technologies. Nature Education; 2008.
Ronaghi M, Karamohamed S, Pettersson B, Uhlen M, Nyren P. Real-time DNA sequencing using detection of pyrophosphate release. Analytical Biochemistry; 1996; 242(1):84–89. doi:10.1006/abio.1996.0432.
Adams CP, Kron SJ. Method for performing amplification of nucleic acid with two primers bound to a single solid support; 1997.
Farinelli L, Kawashima E, Mayer P. Method of nucleic acid amplification. 2007.
Kawashima E, Farinellit L, Mayer P. Method of nucleic acid sequencing. 2004.
Anderson NL, Anderson NG. Proteome and proteomics: new technologies, new concepts, and new words. Electrophoresis; 1998; 19(11):1853–1861. doi:10.1002/elps.1150191103
Blackstock WP, Weir MP. Proteomics: quantitative and physical mapping of cellular proteins. Trends in Biotechnology; 1999; 17(3):121–127. doi:10.1016/S0167-7799(98)01245
Anderson JD, Johansson HJ, Graham CS, Vesterlund M, Pham MT, Bramlett CS, et al. Comprehensive Proteomic Analysis of Mesenchymal Stem Cell Exosomes Reveals Modulation of Angiogenesis via Nuclear Factor-KappaB Signaling. Stem Cells; 2016; 34(3):601–613. doi:10.1002/stem.2298.
Swinbanks D. Government backs proteome proposal. Nature; 1995; 378(6558):653. doi:10.1038/378653a0
36. The Australian Proteome Analysis Facility. www.proteome.org.au. New South Wales, Australia: Macquarie University; 2017.
Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chemical Reviews; 2013; 113(4): 2343–2394. doi:10.1021/cr3003533
Gatto L, Aebersold R, Cox J, Demichev V, Derks J, Emmott E, et al. Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments. Nature Methods; 2023; 20(3):375–386. doi:10.1038/s41592-023-01785-3
Slavov N. Single-cell protein analysis by mass spectrometry. Current Opinion in Chemical Biology. Omics; 2021; 60:1–9. doi:10.1016/j.cbpa.2020.04.018
Holman JD, Dasari S, Tabb DL. Informatics of protein and posttranslational modification detection via shotgun proteomics. Methods Mol Biol; 2013; 1002:167-179. doi:10.1007/978-1-62703-360-2_14
Hood L, Rowen L. The Human Genome Project: big science transforms biology and medicine. Genome Medicine; 2013; 5(9): 79. doi:10.1186/gm483
Chandramouli K, Qian PY. Proteomics: challenges, techniques and possibilities to overcome biological sample complexity. Hum Genomics Proteomics; 2009. doi:10.4061/2009/239204
Yoithapprabhunath TR, Nirmal RM, Santhadevy A, Anusushanth A, Charanya D, Rojiluke, Sri Chinthu KK, Yamunadevi A. Role of proteomics in physiologic and pathologic conditions of dentistry: Overview. J Pharm Bioallied Sci; 2015; 7:S344-S349. doi:10.4103/0975-7406.163448
Pandey A, Mann M. Proteomics to study genes and genomes. Nature;
2000; 405:837-846. doi: 10.1038/35015709
Arbabi Ghahroudi M, Desmyter A, Wyns L, Hamers R, Muyldermans S. Selection and identification of single domain antibody fragments from camel heavy-chain antibodies. FEBS Letters; 1997; 414(3):521–526. doi:10.1016/S0014-5793(97)01062-4
Stumpp MT, Binz HK, Amstutz P. DARPins: A new generation of protein therapeutics. Drug Discovery Today; 2008; 13:695–701. doi:10.1016/j.drudis.2008.04.013
Ayasena SD. Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clinical Chemistry; 1999; 45(9):1628–1650. doi:10.1093/clinchem/45.9.1628
Martin DB, Nelson PS. From genomics to proteomics: techniques and applications in cancer research. Trends Cell Biol; 2001; 11:60-65, doi: 10.1016/s0962-8924(01)02123-7
Krishnankutty R, Bhat A, Azmi A, Souchelnytskyi S, Uddin S. An Overview of Proteomics Techniques and its Application as a Tool in Biomarker and Drug Discovery. J Proteomics Enzymol; 2016; 2:2. doi: 10.4172/2470-1289.1000129
Smith L, Lind MJ, Welham KJ, Cawkwell L. Cancer Biology Proteomics Group. Cancer proteomics and its application to discovery of therapy response markers in human cancer. Cancer; 2006; 107:232-241 doi:10.1002/cncr.22000]
Lahm HW, Langen H. Mass spectrometry: a tool for the identification of proteins separated by gels. Electrophoresis; 2000; 21:2105-2114. doi:10.1002/1522-2683
Vihinen M. Bioinformatics in proteomics. Biomol Eng; 2001; 18:241-248. doi:10.1016/s1389-0344(01)00099-5
He QY, Chiu JF. Proteomics in biomarker discovery and drug development. J Cell Biochem; 2003; 89:868-886. doi:10.1002/jcb.10576
Committee on the Review of Omics-Based Tests for Predicting Patient Outcomes in Clinical Trials; Board on Health Care Services; Board on Health Sciences Policy; Institute of Medicine, Micheel CM, Nass SJ, Omenn GS. Evolution of Translational Omics: Lessons Learned and the Path Forward; 2012. doi:10.17226/13297
Gam LH. Breast cancer and protein biomarkers. World J Exp Med; 2012; 2:86-91 doi:10.5493/wjem.v2.i5.86
Al-Amrani S, Al-Jabri Z, Al-Zaabi A, Alshekaili J, Al-Khabori M. Proteomics: Concepts and applications in human medicine. World Journal of Biological Chemistry; 2021; 12(5):57. doi: 10.4331/wjbc.v12.i5.57
Simpson RJ, Dorow DS. Cancer proteomics: from signaling networks to tumor markers. Trends Biotechnol; 2001; 19:S40-S48. doi: 10.1016/S0167-7799(01)01801-7
Burbaum J, Tobal GM. Proteomics in drug discovery. Curr Opin Chem Biol; 2002; 6: 427-433. doi:10.1016/s1367-5931(02)00337-x]
Jain KK. Innovations, challenges and future prospects of oncoproteomics. Mol Oncol; 2008; 2:153-160. doi: 10.1016/j.molonc.2008.05.003]
Jain KK. Recent advances in clinical oncoproteomics. J Buon; 2007; 12:31-38.
Referanslar
Pearson H. What is a gene?. Nature; 2006;441(7092):398-402.
Demongeot J, Seligmann H. Why is AUG the start codon? Theoretical minimal RNA rings: Maximizing coded information biases 1st codon for the universal initiation codon AUG. Bioessays; 2020; 42(6):1900201. doi: 10.1002/bies.202000061.
Hecht J, Glasgow PR, Jaschke LA, et al. Measurements of translation initiation from all 64 codons in E. coli. Nucleic acids research; 2017;45(7):3615-3626. doi: 10.1093/nar/gkx070.
Başaran E, Aras S, Cansaran-Duman D. Genomik, proteomik metabolomik kavramlarına genel bakış ve uygulama alanları. Türk Hijyen ve Besinsel Biyoloji Dergisi; 2010; 67:85-96.
Winkler H. Verbreitung und Ursache der Parthenogenesis im Pflanzen- und Tierreiche. Verlag Fischer; 1920, Jena.
Nadeau JH, Davisson MT, Doolittle DP, et al. Comparative map for mice and humans. Mammalian Genome; 1992; 3(9):480-536.
Sarwal M, Alemi F. Genomics and Microarray. In: Lotze M, Thomson A (eds.) Measuring Immunity Basic Science and Clinical Practise. Great Britain: Elsevier; 2005. p. 697-706.
Bal SH, Budak F. Genomik, proteomik kavramlarına genel bakış ve uygulama alanları. Uludağ Üniversitesi Tıp Fakültesi Dergisi; 2013; 39(1):65-69.
Fleischmann RD, Adams MD, White O, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science; 1995;269(5223):496-512. doi: 10.1126/science.7542800.
Goffeau A, Barrell BG, Bussey H, et al. Life with 6000 genes. Science; 1996;274:546–567. doi: 10.1126/science.274.5287.546.
The C. elegans Sequencing Consortium. Genome sequence of the nematode, C. elegans: A platform for investing biology. Science; 1998;282:2012–2018. doi: 10.1126/science.282.5396.2012.
Adams MD, Celniker SE, Holt RA, et al. The genome sequence of Drosophila melanogaster. Science; 2000; 287(5461): 2185-2195. doi: 10.1126/science.287.5461.2185.
Allocca M, Zola S, Bellosta P. The fruit fly, Drosophila melanogaster: the making of a model (Part I). In: Perveen FK, (eds.) Drosophila melanogaster: Model for Recent Advances in Genetics and Therapeutics. Rijeka, Croatia: InTech;2018. p.113- 130.
Pandey UB, Nichols CD. Human disease models in Drosophila melanogaster and the role of the fly in therapeutic drug discovery. Pharmacol Rev.; 2011;63:412-431. doi: 10.1124/pr.110.003293.
Baenas N, Wagner AE. Drosophila melanogaster as an alternative model organism in nutrigenomics. Genes Nutr. 2019;14:1-11. doi: 10.1186/s12263-019-0641-y.
Meinke DW, Cherry JM, Dean C, et al. Arabidopsis thaliana: a model plant for genome analysis. Science; 1998; 282(5389):662-682. doi: 10.1126/science.282.5389.662.
Goff SA, Ricke D, Lan TH, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science; 2002; 296(5565): 92-100. doi: 10.1126/science.1068275.
Karami A. Largest and smallest genome in the World; 2013.
Frith MC, Pheasant M, Mattick JS. The amazing complexity of the human transcriptome. European journal of human genetics: EJHG; 2005; 13(8):894-897. doi: 10.1038/sj.ejhg.5201459.
Ateş K. Gen mi, RNA mı?. Deneysel Tıp Araştırma Enstitüsü Dergisi; 6(11):43-49.
Fiers W, Contreras R, Duerinck F, et al. Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene. Nature; 1976; 260(5551):500-507. doi: 10.1038/260500a0.
Nurk S, Koren S, Rhie A, et al. The complete sequence of a human genome. Science; 2022; 376(6588):44-53. doi: 10.1126/science.abj6987.
International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature; 2007; 449(7164):851. doi: 10.1038/nature06258.
International HapMap Consortium. A haplotype map of the human genome. Nature; 2005; 437(7063):1299. doi: doi.org/10.1038/nature04226.
Gibbs RA, Belmont JW, Hardenbol P, et al. The international HapMap project. 2003. doi:10.1038/nature02168.
Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proceedings of the national academy of sciences; 1977; 74(12):5463-5467. doi: 10.1073/pnas.74.12.5463.
Adams JU. DNA Sequencing Technologies. Nature Education; 2008.
Ronaghi M, Karamohamed S, Pettersson B, Uhlen M, Nyren P. Real-time DNA sequencing using detection of pyrophosphate release. Analytical Biochemistry; 1996; 242(1):84–89. doi:10.1006/abio.1996.0432.
Adams CP, Kron SJ. Method for performing amplification of nucleic acid with two primers bound to a single solid support; 1997.
Farinelli L, Kawashima E, Mayer P. Method of nucleic acid amplification. 2007.
Kawashima E, Farinellit L, Mayer P. Method of nucleic acid sequencing. 2004.
Anderson NL, Anderson NG. Proteome and proteomics: new technologies, new concepts, and new words. Electrophoresis; 1998; 19(11):1853–1861. doi:10.1002/elps.1150191103
Blackstock WP, Weir MP. Proteomics: quantitative and physical mapping of cellular proteins. Trends in Biotechnology; 1999; 17(3):121–127. doi:10.1016/S0167-7799(98)01245
Anderson JD, Johansson HJ, Graham CS, Vesterlund M, Pham MT, Bramlett CS, et al. Comprehensive Proteomic Analysis of Mesenchymal Stem Cell Exosomes Reveals Modulation of Angiogenesis via Nuclear Factor-KappaB Signaling. Stem Cells; 2016; 34(3):601–613. doi:10.1002/stem.2298.
Swinbanks D. Government backs proteome proposal. Nature; 1995; 378(6558):653. doi:10.1038/378653a0
36. The Australian Proteome Analysis Facility. www.proteome.org.au. New South Wales, Australia: Macquarie University; 2017.
Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chemical Reviews; 2013; 113(4): 2343–2394. doi:10.1021/cr3003533
Gatto L, Aebersold R, Cox J, Demichev V, Derks J, Emmott E, et al. Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments. Nature Methods; 2023; 20(3):375–386. doi:10.1038/s41592-023-01785-3
Slavov N. Single-cell protein analysis by mass spectrometry. Current Opinion in Chemical Biology. Omics; 2021; 60:1–9. doi:10.1016/j.cbpa.2020.04.018
Holman JD, Dasari S, Tabb DL. Informatics of protein and posttranslational modification detection via shotgun proteomics. Methods Mol Biol; 2013; 1002:167-179. doi:10.1007/978-1-62703-360-2_14
Hood L, Rowen L. The Human Genome Project: big science transforms biology and medicine. Genome Medicine; 2013; 5(9): 79. doi:10.1186/gm483
Chandramouli K, Qian PY. Proteomics: challenges, techniques and possibilities to overcome biological sample complexity. Hum Genomics Proteomics; 2009. doi:10.4061/2009/239204
Yoithapprabhunath TR, Nirmal RM, Santhadevy A, Anusushanth A, Charanya D, Rojiluke, Sri Chinthu KK, Yamunadevi A. Role of proteomics in physiologic and pathologic conditions of dentistry: Overview. J Pharm Bioallied Sci; 2015; 7:S344-S349. doi:10.4103/0975-7406.163448
Pandey A, Mann M. Proteomics to study genes and genomes. Nature;
2000; 405:837-846. doi: 10.1038/35015709
Arbabi Ghahroudi M, Desmyter A, Wyns L, Hamers R, Muyldermans S. Selection and identification of single domain antibody fragments from camel heavy-chain antibodies. FEBS Letters; 1997; 414(3):521–526. doi:10.1016/S0014-5793(97)01062-4
Stumpp MT, Binz HK, Amstutz P. DARPins: A new generation of protein therapeutics. Drug Discovery Today; 2008; 13:695–701. doi:10.1016/j.drudis.2008.04.013
Ayasena SD. Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clinical Chemistry; 1999; 45(9):1628–1650. doi:10.1093/clinchem/45.9.1628
Martin DB, Nelson PS. From genomics to proteomics: techniques and applications in cancer research. Trends Cell Biol; 2001; 11:60-65, doi: 10.1016/s0962-8924(01)02123-7
Krishnankutty R, Bhat A, Azmi A, Souchelnytskyi S, Uddin S. An Overview of Proteomics Techniques and its Application as a Tool in Biomarker and Drug Discovery. J Proteomics Enzymol; 2016; 2:2. doi: 10.4172/2470-1289.1000129
Smith L, Lind MJ, Welham KJ, Cawkwell L. Cancer Biology Proteomics Group. Cancer proteomics and its application to discovery of therapy response markers in human cancer. Cancer; 2006; 107:232-241 doi:10.1002/cncr.22000]
Lahm HW, Langen H. Mass spectrometry: a tool for the identification of proteins separated by gels. Electrophoresis; 2000; 21:2105-2114. doi:10.1002/1522-2683
Vihinen M. Bioinformatics in proteomics. Biomol Eng; 2001; 18:241-248. doi:10.1016/s1389-0344(01)00099-5
He QY, Chiu JF. Proteomics in biomarker discovery and drug development. J Cell Biochem; 2003; 89:868-886. doi:10.1002/jcb.10576
Committee on the Review of Omics-Based Tests for Predicting Patient Outcomes in Clinical Trials; Board on Health Care Services; Board on Health Sciences Policy; Institute of Medicine, Micheel CM, Nass SJ, Omenn GS. Evolution of Translational Omics: Lessons Learned and the Path Forward; 2012. doi:10.17226/13297
Gam LH. Breast cancer and protein biomarkers. World J Exp Med; 2012; 2:86-91 doi:10.5493/wjem.v2.i5.86
Al-Amrani S, Al-Jabri Z, Al-Zaabi A, Alshekaili J, Al-Khabori M. Proteomics: Concepts and applications in human medicine. World Journal of Biological Chemistry; 2021; 12(5):57. doi: 10.4331/wjbc.v12.i5.57
Simpson RJ, Dorow DS. Cancer proteomics: from signaling networks to tumor markers. Trends Biotechnol; 2001; 19:S40-S48. doi: 10.1016/S0167-7799(01)01801-7
Burbaum J, Tobal GM. Proteomics in drug discovery. Curr Opin Chem Biol; 2002; 6: 427-433. doi:10.1016/s1367-5931(02)00337-x]
Jain KK. Innovations, challenges and future prospects of oncoproteomics. Mol Oncol; 2008; 2:153-160. doi: 10.1016/j.molonc.2008.05.003]
Jain KK. Recent advances in clinical oncoproteomics. J Buon; 2007; 12:31-38.
