CAGE: cap analysis of gene expression

被引:263
作者
Kodzius, R
Kojima, M
Nishiyori, H
Nakamura, M
Fukuda, S
Tagami, M
Sasaki, D
Imamura, K
Kai, C
Harbers, M
Hayashizaki, Y
Carninci, P
机构
[1] RIKEN Genom Sci Ctr, Yokohama Inst, Lab Genome Explorat Res Grp, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan
[2] RIKEN, Genome Sci Lab, Wako, Saitama 3510198, Japan
[3] Tsukuba Branch, Ibaraki 3000332, Japan
关键词
D O I
10.1038/nmeth0306-211
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Transcript abundance can be determined by various methods, including reverse transcription (RT)-PCR, microarray analysis, sequencing of expressed sequence tags (ESTs), serial analysis of gene expression (SAGE) and massively parallel signature sequencing (MPSS)(1,2), most of which rely on 3' end-related sequences. But for the identification of transcription start sites (TSSs) and their associated promoters, 5' end-specific signature sequences are required for higher annotations of expression profiles. Therefore, we and others began cloning of short sequence tags from the 5' ends of cDNAs, using cap analysis of gene expression (CAGE)(3) and 5'-SAGE(4,5). In these techniques linkers are attached to the 5' ends of full-length enriched cDNAs to introduce a recognition site for the restriction endonuclease MmeI adjacent to the 5' ends. MmeI cleaves cDNAs at a sequence 20 and 18 nucleotides away (3') from its recognition site, creating a two-base overhang. After amplification, the sequencing tags are concatenated for high-throughput sequencing (Fig. 1). Here we present a CAGE protocol that has been used extensively for high-throughput analysis of mouse and human transcripts. The method includes new features for improved library construction, such as the use of random priming(6) for gene discovery from nonpolyadenylated RNA, simplified full-length cDNA enrichment by multiwell filtration-based cap-trapping and a pooling strategy for high-throughput CAGE library preparation. The application of this CAGE protocol will contribute to genome annotation, gene discovery and expression profiling(7).
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页码:211 / 222
页数:12
相关论文
共 16 条
[1]   Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays [J].
Brenner, S ;
Johnson, M ;
Bridgham, J ;
Golda, G ;
Lloyd, DH ;
Johnson, D ;
Luo, SJ ;
McCurdy, S ;
Foy, M ;
Ewan, M ;
Roth, R ;
George, D ;
Eletr, S ;
Albrecht, G ;
Vermaas, E ;
Williams, SR ;
Moon, K ;
Burcham, T ;
Pallas, M ;
DuBridge, RB ;
Kirchner, J ;
Fearon, K ;
Mao, J ;
Corcoran, K .
NATURE BIOTECHNOLOGY, 2000, 18 (06) :630-634
[2]  
Carninci P, 1999, METHOD ENZYMOL, V303, P19
[3]   High-efficiency full-length cDNA cloning by biotinylated CAP trapper [J].
Carninci, P ;
Kvam, C ;
Kitamura, A ;
Ohsumi, T ;
Okazaki, Y ;
Itoh, M ;
Kamiya, M ;
Shibata, K ;
Sasaki, N ;
Izawa, M ;
Muramatsu, M ;
Hayashizaki, Y ;
Schneider, C .
GENOMICS, 1996, 37 (03) :327-336
[4]   The transcriptional landscape of the mammalian genome [J].
Carninci, P ;
Kasukawa, T ;
Katayama, S ;
Gough, J ;
Frith, MC ;
Maeda, N ;
Oyama, R ;
Ravasi, T ;
Lenhard, B ;
Wells, C ;
Kodzius, R ;
Shimokawa, K ;
Bajic, VB ;
Brenner, SE ;
Batalov, S ;
Forrest, ARR ;
Zavolan, M ;
Davis, MJ ;
Wilming, LG ;
Aidinis, V ;
Allen, JE ;
Ambesi-Impiombato, X ;
Apweiler, R ;
Aturaliya, RN ;
Bailey, TL ;
Bansal, M ;
Baxter, L ;
Beisel, KW ;
Bersano, T ;
Bono, H ;
Chalk, AM ;
Chiu, KP ;
Choudhary, V ;
Christoffels, A ;
Clutterbuck, DR ;
Crowe, ML ;
Dalla, E ;
Dalrymple, BP ;
de Bono, B ;
Della Gatta, G ;
di Bernardo, D ;
Down, T ;
Engstrom, P ;
Fagiolini, M ;
Faulkner, G ;
Fletcher, CF ;
Fukushima, T ;
Furuno, M ;
Futaki, S ;
Gariboldi, M .
SCIENCE, 2005, 309 (5740) :1559-1563
[5]   Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution [J].
Cheng, J ;
Kapranov, P ;
Drenkow, J ;
Dike, S ;
Brubaker, S ;
Patel, S ;
Long, J ;
Stern, D ;
Tammana, H ;
Helt, G ;
Sementchenko, V ;
Piccolboni, A ;
Bekiranov, S ;
Bailey, DK ;
Ganesh, M ;
Ghosh, S ;
Bell, I ;
Gerhard, DS ;
Gingeras, TR .
SCIENCE, 2005, 308 (5725) :1149-1154
[6]   5′-end SAGE for the analysis of transcriptional start sites [J].
Hashimoto, S ;
Suzuki, Y ;
Kasai, Y ;
Morohoshi, K ;
Yamada, T ;
Sese, J ;
Morishita, S ;
Sugano, S ;
Matsushima, K .
NATURE BIOTECHNOLOGY, 2004, 22 (09) :1146-1149
[7]   Use of transcriptional sequencing in difficult to read areas of the genome [J].
Ishikawa, T ;
Hayashida, Y ;
Hirayasu, K ;
Ozawa, K ;
Yamamoto, N ;
Tanaka, T ;
Matsuura, S .
ANALYTICAL BIOCHEMISTRY, 2003, 316 (02) :202-207
[8]   NONCOOPERATIVITY OF BIOTIN BINDING TO TETRAMERIC STREPTAVIDIN [J].
JONES, ML ;
KURZBAN, GP .
BIOCHEMISTRY, 1995, 34 (37) :11750-11756
[9]   Antisense transcription in the mammalian transcriptome [J].
Katayama, S ;
Tomaru, Y ;
Kasukawa, T ;
Waki, K ;
Nakanishi, M ;
Nakamura, M ;
Nishida, H ;
Yap, CC ;
Suzuki, M ;
Kawai, J ;
Suzuki, H ;
Carninci, P ;
Hayashizaki, Y ;
Wells, C ;
Frith, M ;
Ravasi, T ;
Pang, KC ;
Hallinan, J ;
Mattick, J ;
Hume, DA ;
Lipovich, L ;
Batalov, S ;
Engström, PG ;
Mizuno, Y ;
Faghihi, MA ;
Sandelin, A ;
Chalk, AM ;
Mottagui-Tabar, S ;
Liang, Z ;
Lenhard, B ;
Wahlestedt, C .
SCIENCE, 2005, 309 (5740) :1564-1566
[10]   Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags [J].
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 .
FEBS LETTERS, 2004, 559 (1-3) :22-26