Applications of next-generation sequencing technologies in functional genomics

被引:800
作者
Morozova, Olena [1 ]
Marra, Marco A. [1 ]
机构
[1] BC Canc Agcy Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada
基金
加拿大自然科学与工程研究理事会;
关键词
Illumina/Solexa; ABI/SOLiD; 454/Roche; Functional genomics; Next-generation sequencing technology; Transcriptome; Epigenome; Deep sequencing; Sequencing by synthesis; Sequencing by ligation;
D O I
10.1016/j.ygeno.2008.07.001
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
A new generation of sequencing technologies, from Illumina/Solexa, ABI/SOLiD, 454/Roche, and Helicos, has provided unprecedented opportunities for high-throughput functional genomic research. To date, these technologies have been applied in a variety of contexts, including whole-genome sequencing, targeted resequencing, discovery of transcription factor binding sites, and noncoding RNA expression profiling. This review discusses applications of next-generation sequencing technologies in functional genomics research and highlights the transforming potential these technologies offer. (C) 2008 Elsevier Inc. All rights reserved.
引用
收藏
页码:255 / 264
页数:10
相关论文
共 111 条
[51]   Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin [J].
Johnson, Steven M. ;
Tan, Frederick J. ;
McCullough, Heather L. ;
Riordan, Daniel P. ;
Fire, Andrew Z. .
GENOME RESEARCH, 2006, 16 (12) :1505-1516
[52]   Genome-wide expression profiling of the Arabidopsis female gametophyte identifies families of small, secreted proteins [J].
Jones-Rhoades, Matthew W. ;
Borevitz, Justin O. ;
Preuss, Daphne .
PLOS GENETICS, 2007, 3 (10) :1848-1861
[53]   Genome-wide profiling and analysis of Arabidopsis siRNAs [J].
Kasschau, Kristin D. ;
Fahlgren, Noah ;
Chapman, Elisabeth J. ;
Sullivan, Christopher M. ;
Cumbie, Jason S. ;
Givan, Scott A. ;
Carrington, James C. .
PLOS BIOLOGY, 2007, 5 (03) :479-493
[54]  
Korbel JO, 2007, SCIENCE, V318, P420, DOI 10.1126/science.1149504
[55]   In vivo cross-linking and immunoprecipitation for studying dynamic protein:: DNA associations in chromatin environment [J].
Kuo, MH ;
Allis, CD .
METHODS-A COMPANION TO METHODS IN ENZYMOLOGY, 1999, 19 (03) :425-433
[56]   Initial sequencing and analysis of the human genome [J].
Lander, ES ;
Int Human Genome Sequencing Consortium ;
Linton, LM ;
Birren, B ;
Nusbaum, C ;
Zody, MC ;
Baldwin, J ;
Devon, K ;
Dewar, K ;
Doyle, M ;
FitzHugh, W ;
Funke, R ;
Gage, D ;
Harris, K ;
Heaford, A ;
Howland, J ;
Kann, L ;
Lehoczky, J ;
LeVine, R ;
McEwan, P ;
McKernan, K ;
Meldrim, J ;
Mesirov, JP ;
Miranda, C ;
Morris, W ;
Naylor, J ;
Raymond, C ;
Rosetti, M ;
Santos, R ;
Sheridan, A ;
Sougnez, C ;
Stange-Thomann, N ;
Stojanovic, N ;
Subramanian, A ;
Wyman, D ;
Rogers, J ;
Sulston, J ;
Ainscough, R ;
Beck, S ;
Bentley, D ;
Burton, J ;
Clee, C ;
Carter, N ;
Coulson, A ;
Deadman, R ;
Deloukas, P ;
Dunham, A ;
Dunham, I ;
Durbin, R ;
French, L .
NATURE, 2001, 409 (6822) :860-921
[57]   Characterization of the piRNA complex from rat testes [J].
Lau, Nelson C. ;
Seto, Anita G. ;
Kim, Jinkuk ;
Kuramochi-Miyagawa, Satomi ;
Nakano, Toru ;
Bartel, David P. ;
Kingston, Robert E. .
SCIENCE, 2006, 313 (5785) :363-367
[58]   THE C-ELEGANS HETEROCHRONIC GENE LIN-4 ENCODES SMALL RNAS WITH ANTISENSE COMPLEMENTARITY TO LIN-14 [J].
LEE, RC ;
FEINBAUM, RL ;
AMBROS, V .
CELL, 1993, 75 (05) :843-854
[59]   Elucidation of the small RNA component of the transcriptome [J].
Lu, C ;
Tej, SS ;
Luo, SJ ;
Haudenschild, CD ;
Meyers, BC ;
Green, PJ .
SCIENCE, 2005, 309 (5740) :1567-1569
[60]   MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant [J].
Lu, Cheng ;
Kulkarni, Karthik ;
Souret, Frederic F. ;
MuthuValliappan, Ramesh ;
Tej, Shivakundan Singh ;
Poethig, R. Scott ;
Henderson, Ian R. ;
Jacobsen, Steven E. ;
Wang, Wenzhong ;
Green, Pamela J. ;
Meyers, Blake C. .
GENOME RESEARCH, 2006, 16 (10) :1276-1288