Yeni Nesil DNA Dizileme

Year 2011, Volume: 1 Issue: 1, 11 - 18, 25.10.2011

Duran Üstek Neslihan Abacı Sema Sırma Aris Çakiris

Abstract

Yeni nesil dizileme; genom, transkriptom, DNA-protein etkileşimlerinin geniş kapsamlı
analizini ucuz, rutin ve yaygın hale dönüştürdüğünden biyolojik araştırmaları önemli ölçüde
hızlandırma potansiyeline sahiptir. Yeni nesil dizileme teknolojisi; mRNA, küçük RNA
profili, transkripsiyon faktör bağlanma bölgelerinin genom boyu karakterizasyonu, kromatin
yapısı ve metilasyon paterni, atasal DNA mikrobiyolojisi ve metagenomik için yeni ve hızlı
yollar sağlar. Bu makalede yeni nesil dizileme teknolojileri, yeni nesil dizileme sistemlerindeki
yeni gelişmeler ve yeni nesil dizileme teknolojisinin uygulama alanları tartışılmıştır.

References

• Margulies M, Egholm M, Airman WE, Attiya S, Bader JS, Bemben LA, et.al.. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005 Sep 15;437(7057):376-80
• Venter JC, Adams MD, Sutton GG, Kerlavage AR, Smith HO, Hunkapiller M. Shotgun sequencing of the human genome. Science 1998, 280,1540-1542
• Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, The genome sequence of Drosophila melanogaster. Science. 2000 Mar 24;287(5461):2185-95
• Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995 Jul28;269(5223):496-512
• Sanger F, Nicklen S, and Coulson AR. DNA sequencing with cham-terminating inhibitors. Proc. Natl.Acad. Sei. 1977; 74:5463-5467
• Ronaghi M, Nygren M, Lundeberg J, Nyren P. Analyses of secondary structures in DNA by pyrosequencing. Anal Biochem. 1999; Feb 1;267(1):65-71
• http://454.com/downloads/my454/documentation/gsflx/method-manuals/GS-FLX-Titanium-emPCR-MethodManual-(Apr2009)
• Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res. 2001; Jan;ll(l):3-ll
• Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008; 452: 872-877
• N4 Green RE, Krause J, Ptak SE, Briggs AW, Ronan MT, Simons JF, et al. Analysis of one million base pairs of Neanderthal DNA. Nature 2006; 444: 330-336
• Gilbert MT, Binladen J, Miller W, Wiuf C, Willerslev E, Poinar H, et al. Recharacterization of ancient DNA miscodinglesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Res. 2007;35(1):1-10
• Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 2008; 9: 387^402
• Schuster SC. Next-generation sequencing transforms today's biology. Nat. Methods 2008. 5 (1): 16-8
• Rusk N. Torrents of sequence. Nature Methods 2011; 8(1)44
• Treffer R, Deckert V. Recent advances in singlemolecule sequencing. Current Opinion in Biotechnology 2010; 21( 1): 4-11
• Cox-Foster DL, Conlan S, Holmes EC, Palacios G, Evans JD, Moran NA, Quan PL, Briese T, Hornig M, Geiser DM, Martinson V, vanEngelsdorp D, Kalkstein AL, Drysdale A, Hui J, Zhai J, Cui L, Hutchison SK, Simons JF, Egholm M, Pettis JS, Lipkin WI. A metagenomic survey of microbes in honey bee colony collapse disorder. Science. 2007 Oct 12;318(5848):283-7.
• Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Marchs ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Center for Genome Sciences, Washington University, St. Louis, Missouri 63108, USA. Nature. 2006 Dec 21;444(7122):1027-31.
• Weber AP, Weber KL, Carr K, Wilkerson C, Ohlrogge JB. Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiology 2007; 144: 32-42
• Novaes E, Drost DR, Farmerie WG, Pappas GJ Jr, Grattapaglia D, Sederoff RR, Kirst M. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 2008; 9: 312
• Bekal S, Craig JP, Hudson ME, Niblack TL, Domier LL, Lambert KN. Genomic DNA sequence comparison between two inbred soybean cyst nematode biotypes facilitated by massively parallel 454 micro-bead sequencing. Molecular Genetic and Genomics 2008; 279: 535-543
• Green RE, Malaspinas AS, Krause J, Briggs AW, Johnson PL, Uhler C, Meyer M, Good JM. A complete Neanderthal mitochondrial genome sequence determined by high-throughput sequencing. Cell 2008; 134: 416-426
• Ng P, Tan JJ, Ooi HS, Lee YL, Chiu KP, Fullwood MJ, Srinivasan KG, Perbost C, Du L, Sung WK, Wei CL, Ruan Y. Multiplex sequencing of paired-end ditags (MS-PET) : a strategy for he ultra -high -throughput analysis of transcriptomes and genomes. Nucleic acids res. 2006; 13;34(12):e84
• Ng P, Wei CL, Ruan Y. Paired -end ditagging for transcriptome and genome analysis. Curr. Protoc. Mol. Biol.2007; 21,12
• Beldade P, Rudd S, Gruber JD, Long AD. A wing expressed sequence tag resource for bicyclus anynana butterflies, an evo-devo model. BMC Genomics 2006; 7,130
• Sugarbaker DJ, Richards WG, Gordon GJ, Dong L, De Rienzo A, Maulik G, Glickman JN, Chirieac LR, Hartman ML, Taillon BE, Du L, Transcriptome sequencing of malignant pleural mesothelioma tumors. Proc. Natl. Acad. Sci. USA 2008; 105, 3521-3526
• Toth AL, Varala K, Newman TC, Miguez FE, Hutchison SK, Willoughby DA, Simons JF, Egholm M, Hunt JH, Hudson ME, Robinson GE. Wasp gene expression sopports an evolutionary link between maternal behavior and eusociahty. Science 2007; 318,441-444
• Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, Ronaghi M, Fire AZ. A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Research 2007; 35: el30
• Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, Obata Y, Chiba H, Kohara Y, Kono T, Nakano T, Surani MA, Sakaki Y, Sasaki H. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 2008; 453:539-43
• Taylor KH, Kramer RS, Davis JW, Guo J, Duff DJ, Xu D, Caldwell CW, Shi H. Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res. 2007 Sep; 15;67(18):8511-8
• Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007 Aug; 4(8):651-7
• Wang JC. Finding primary targets of transcriptional regulators. Cell Cycle. 2005 Mar; 4(3):356-8
• Buisine N, Sachs L. Impact of genome assembly status on ChlP-Seq and ChlP-PET data mapping. BMC Res Notes. 2009 Dec; 16;2:257
• Farnham PJ. Insights from genomic profiling of transcription factors. Nat Rev Genet. 2009 Sep; 10(9):605-16