Genler ve Genomlar
Özet
Bu bölümde, yaşadığımız evrende bulunan çeşitli genom türlerinin anatomilerini inceleyeceğiz. Genom anatomisini inceleyeceğimiz temel başlık şunlardır: Ökaryotik nüklear genomlar: Bu kategoride insan genomu gibi ökaryotik organizmaların nükleer genomları yer alır. Ökaryotik genomlar kompleks yapılara sahip olup çekirdek içinde yer alır. İnsan genomu, yaklaşık 3 milyar baz çiftinden oluşan bir DNA molekülüdür ve genlerin yanı sıra düzenleyici bölgeler, tekrarlı diziler ve diğer genomik öğeleri içerir. Ökaryotik organellerin genomları: Bu kategori prokaryotların (bakteri ve arke) genomlarını ve ökaryotik organellerin (mitokondri ve kloroplast gibi) genomlarını içerir. Prokaryotik genomlar, tek bir dairesel kromozom şeklinde bulunur ve genellikle daha küçük boyuttadır. Ökaryotik organeller ise bağımsız olarak evrimleşmiş ve eski prokaryotlardan türemiştir. Bu organellerin genomları da dairesel yapıda olup genellikle daha küçüktür. Hareketli genetik elementler: Bu kategoride viral genomlar ve hareketli genetik elementler (transpozonlar) gruplandırılacaktır. Virüsler, genellikle protein kaplamalara sahip küçük genomlardır ve hücreleri enfekte ederek çoğalırlar. Hareketli genetik elementler ise DNA veya RNA formunda olan genetik parçalardır ve konak genomuna entegre olabilen ve kopyalanabilen özelliklere sahiptirler. Bu üç tür genom anatomisi, farklı organizmaların genomlarının yapısal ve işlevsel özelliklerini anlamamıza yardımcı olur ve genetik çeşitliliği incelememize olanak tanır.
Referanslar
Y. Chen, M.E. Hoover, X. Dang, A.A. Shomo, X. Guan, A.G. Marshall, M.A. Freitas, N.L. Young, Quantitative mass spectrometry reveals that intact histone H1 phosphorylations are variant specific and exhibit single molecule hierarchical dependence, Molecular & Cel- lular Proteomics, 15 (2016) 818-833.
G.P. Copenhaver, K. Nickel, T. Kuromori, M.-I. Benito, S. Kaul, X. Lin, M. Bevan, G. Murp- hy, B. Harris, L.D. Parnell, Genetic definition and sequence analysis of Arabidopsis centro- meres, Science, 286 (1999) 2468-2474.
A.R. Cutter, J.J. Hayes, A brief review of nucleosome structure, FEBS letters, 589 (2015) 2914-2922.
T. De Lange, Shelterin: the protein complex that shapes and safeguards human telomeres, Genes & development, 19 (2005) 2100-2110.
P.J. Robinson, D. Rhodes, Structure of the ‘30 nm’chromatin fibre: a key role for the linker histone, Current opinion in structural biology, 16 (2006) 336-343.
M.G. Schueler, A.W. Higgins, M.K. Rudd, K. Gustashaw, H.F. Willard, Genomic and gene- tic definition of a functional human centromere, Science, 294 (2001) 109-115.
A. Travers, The location of the linker histone on the nucleosome, Trends in biochemical sciences, 24 (1999) 4-7.
G. Bernardi, The isochore organization of the human genome, Annual review of genetics, 23 (1989) 637-659.
E. Elhaik, D. Graur, A comparative study and a phylogenetic exploration of the compo- sitional architectures of mammalian nuclear genomes, PLoS Computational Biology, 10 (2014) e1003925.
I. Ovcharenko, G.G. Loots, M.A. Nobrega, R.C. Hardison, W. Miller, L. Stubbs, Evolution and functional classification of vertebrate gene deserts, Genome research, 15 (2005) 137- 145.
M. Costantini, O. Clay, F. Auletta, G. Bernardi, An isochore map of human chromosomes, Genome research, 16 (2006) 536-541.
A.G.I.g.t.o.g.g. de, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, nature, 408 (2000) 796-815.
M. Ashburner, C.M. Bergman, Drosophila melanogaster: a case study of a model genomic sequence and its consequences, Genome research, 15 (2005) 1661-1667.
S. Istrail, G.G. Sutton, L. Florea, A.L. Halpern, C.M. Mobarry, R. Lippert, B. Walenz, H. Shatkay, I. Dew, J.R. Miller, Whole-genome shotgun assembly and comparison of human genome assemblies, Proceedings of the National Academy of Sciences, 101 (2004) 1916- 1921.
N. Naidoo, Y. Pawitan, R. Soong, D.N. Cooper, C.-S. Ku, Human genetics and genomics a decade after the release of the draft sequence of the human genome, Human genomics, 5 (2011) 1-46.
Iniative, A. G. (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408(6814), 796-815.
Project management: Fulton Lucinda A. 1 Mardis Elaine R. 1 Wilson Richard K. 1. (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432(7018), 695-716.
B. Dujon, The yeast genome project: what did we learn?, Trends in Genetics, 12 (1996) 263-270.
L. Duret, tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes, Trends in Genetics, 16 (2000) 287-289.
J. Xu, J. Zhang, Are human translated pseudogenes functional? Molecular Biology and Evo- lution, 33 (2015) 755-760.
Y. Tutar, Pseudogenes, International Journal of Genomics, 2012 (2012).
L. Poliseno, L. Salmena, J. Zhang, B. Carver, W.J. Haveman, P.P. Pandolfi, A coding-inde- pendent function of gene and pseudogene mRNAs regulates tumour biology, Nature, 465 (2010) 1033-1038.
D.A. Petrov, Evolution of genome size: new approaches to an old problem, TRENDS in Genetics, 17 (2001) 23-28.
B.A. Payseur, P. Jing, R.J. Haasl, A genomic portrait of human microsatellite variation, Mo- lecular biology and evolution, 28 (2011) 303-312.
A.K. Csink, S. Henikoff, Something from nothing: the evolution and utility of satellite re- peats, Trends in Genetics, 14 (1998) 200-204.
P.J. Keeling, J.M. Archibald, Organelle evolution: what’s in a name? Current biology, 18 (2008) R345-R347.
L. Margulis, Origin of eukaryotic cells: evidence and research implications for a theory of the origin and evolution of microbial, plant, and animal cells on the Precambrian earth, (No Title), (1970).
B.F. Lang, M.W. Gray, G. Burger, Mitochondrial genome evolution and the origin of eukar- yotes, Annual review of genetics, 33 (1999) 351-397.
J.D. Palmer, Comparative organization of chloroplast genomes, Annual review of genetics, 19 (1985) 325-354.
Takahashi, T., Nishida, T., Tuji, A. et al. Delineation of six species of the primitive algal genus Glaucocystis based on in situ ultrastructural characteristics. Sci Rep 6, 29209 (2016).
Muñoz-López M, García-Pérez JL. DNA transposons: nature and applications in genomics. Curr Genomics. 2010 Apr;11(2):115-28.
Frazer K A, Chen X, Hinds D A, Pant P V, Patil N, Cox D R. Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates. Genome Res. 2003;13(3):341–346.
Nekrutenko A, Li W H. Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 2001;17(11):619–621.
Referanslar
Y. Chen, M.E. Hoover, X. Dang, A.A. Shomo, X. Guan, A.G. Marshall, M.A. Freitas, N.L. Young, Quantitative mass spectrometry reveals that intact histone H1 phosphorylations are variant specific and exhibit single molecule hierarchical dependence, Molecular & Cel- lular Proteomics, 15 (2016) 818-833.
G.P. Copenhaver, K. Nickel, T. Kuromori, M.-I. Benito, S. Kaul, X. Lin, M. Bevan, G. Murp- hy, B. Harris, L.D. Parnell, Genetic definition and sequence analysis of Arabidopsis centro- meres, Science, 286 (1999) 2468-2474.
A.R. Cutter, J.J. Hayes, A brief review of nucleosome structure, FEBS letters, 589 (2015) 2914-2922.
T. De Lange, Shelterin: the protein complex that shapes and safeguards human telomeres, Genes & development, 19 (2005) 2100-2110.
P.J. Robinson, D. Rhodes, Structure of the ‘30 nm’chromatin fibre: a key role for the linker histone, Current opinion in structural biology, 16 (2006) 336-343.
M.G. Schueler, A.W. Higgins, M.K. Rudd, K. Gustashaw, H.F. Willard, Genomic and gene- tic definition of a functional human centromere, Science, 294 (2001) 109-115.
A. Travers, The location of the linker histone on the nucleosome, Trends in biochemical sciences, 24 (1999) 4-7.
G. Bernardi, The isochore organization of the human genome, Annual review of genetics, 23 (1989) 637-659.
E. Elhaik, D. Graur, A comparative study and a phylogenetic exploration of the compo- sitional architectures of mammalian nuclear genomes, PLoS Computational Biology, 10 (2014) e1003925.
I. Ovcharenko, G.G. Loots, M.A. Nobrega, R.C. Hardison, W. Miller, L. Stubbs, Evolution and functional classification of vertebrate gene deserts, Genome research, 15 (2005) 137- 145.
M. Costantini, O. Clay, F. Auletta, G. Bernardi, An isochore map of human chromosomes, Genome research, 16 (2006) 536-541.
A.G.I.g.t.o.g.g. de, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, nature, 408 (2000) 796-815.
M. Ashburner, C.M. Bergman, Drosophila melanogaster: a case study of a model genomic sequence and its consequences, Genome research, 15 (2005) 1661-1667.
S. Istrail, G.G. Sutton, L. Florea, A.L. Halpern, C.M. Mobarry, R. Lippert, B. Walenz, H. Shatkay, I. Dew, J.R. Miller, Whole-genome shotgun assembly and comparison of human genome assemblies, Proceedings of the National Academy of Sciences, 101 (2004) 1916- 1921.
N. Naidoo, Y. Pawitan, R. Soong, D.N. Cooper, C.-S. Ku, Human genetics and genomics a decade after the release of the draft sequence of the human genome, Human genomics, 5 (2011) 1-46.
Iniative, A. G. (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408(6814), 796-815.
Project management: Fulton Lucinda A. 1 Mardis Elaine R. 1 Wilson Richard K. 1. (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432(7018), 695-716.
B. Dujon, The yeast genome project: what did we learn?, Trends in Genetics, 12 (1996) 263-270.
L. Duret, tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes, Trends in Genetics, 16 (2000) 287-289.
J. Xu, J. Zhang, Are human translated pseudogenes functional? Molecular Biology and Evo- lution, 33 (2015) 755-760.
Y. Tutar, Pseudogenes, International Journal of Genomics, 2012 (2012).
L. Poliseno, L. Salmena, J. Zhang, B. Carver, W.J. Haveman, P.P. Pandolfi, A coding-inde- pendent function of gene and pseudogene mRNAs regulates tumour biology, Nature, 465 (2010) 1033-1038.
D.A. Petrov, Evolution of genome size: new approaches to an old problem, TRENDS in Genetics, 17 (2001) 23-28.
B.A. Payseur, P. Jing, R.J. Haasl, A genomic portrait of human microsatellite variation, Mo- lecular biology and evolution, 28 (2011) 303-312.
A.K. Csink, S. Henikoff, Something from nothing: the evolution and utility of satellite re- peats, Trends in Genetics, 14 (1998) 200-204.
P.J. Keeling, J.M. Archibald, Organelle evolution: what’s in a name? Current biology, 18 (2008) R345-R347.
L. Margulis, Origin of eukaryotic cells: evidence and research implications for a theory of the origin and evolution of microbial, plant, and animal cells on the Precambrian earth, (No Title), (1970).
B.F. Lang, M.W. Gray, G. Burger, Mitochondrial genome evolution and the origin of eukar- yotes, Annual review of genetics, 33 (1999) 351-397.
J.D. Palmer, Comparative organization of chloroplast genomes, Annual review of genetics, 19 (1985) 325-354.
Takahashi, T., Nishida, T., Tuji, A. et al. Delineation of six species of the primitive algal genus Glaucocystis based on in situ ultrastructural characteristics. Sci Rep 6, 29209 (2016).
Muñoz-López M, García-Pérez JL. DNA transposons: nature and applications in genomics. Curr Genomics. 2010 Apr;11(2):115-28.
Frazer K A, Chen X, Hinds D A, Pant P V, Patil N, Cox D R. Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates. Genome Res. 2003;13(3):341–346.
Nekrutenko A, Li W H. Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 2001;17(11):619–621.
