5-Cap Selection Methods and Their Application in Full-Length cDNA Library Construction and Transcription Start Site Profiling

doi:10.1007/s12204-014-1545-z

上海交通大学学报（英文版） ›› 2014, Vol. 19 ›› Issue (5): 580-586.doi: 10.1007/s12204-014-1545-z

5-Cap Selection Methods and Their Application in Full-Length cDNA Library Construction and Transcription Start Site Profiling

BAI Ling* (白玲), WANG Qi (王琪), LI Hong-mei (李红梅),CHENG Ming (程酩), ZHANG Ning-bo (张宁波), LI Hua* (李华)

(School of Biomedical Engineering, Shanghai Jiaotong University, Shanghai 200240, China)

出版日期:2014-10-31 发布日期:2014-11-12
通讯作者: BAI Ling(白玲), LI Hua (李华) E-mail:kaikaixinxin@sjtu.edu.cn, lbai@sjtu.edu.cn

5-Cap Selection Methods and Their Application in Full-Length cDNA Library Construction and Transcription Start Site Profiling

BAI Ling* (白玲), WANG Qi (王琪), LI Hong-mei (李红梅),CHENG Ming (程酩), ZHANG Ning-bo (张宁波), LI Hua* (李华)

(School of Biomedical Engineering, Shanghai Jiaotong University, Shanghai 200240, China)

Online:2014-10-31 Published:2014-11-12
Contact: BAI Ling(白玲), LI Hua (李华) E-mail:kaikaixinxin@sjtu.edu.cn, lbai@sjtu.edu.cn

摘要/Abstract

摘要： With the accomplishment of the genome draft sequences, identification of functional elements in genome has become an urgent task. Full-length cDNAs provide an important resource for gene identification and their precise structural feature determination. It also provides a basis for genomic element definition. As many regulatory elements are around transcription start sites (TSSs), precise localization of TSSs in the genome becomes a critical step for identifying the associated core promoters. Massive parallel snapshot of TSSs at a particular time under a specific experimental condition makes it possible to globally analyze important regulatory elements around TSSs and further construct transcriptional regulatory networks. In this paper, we first reviewed two important full-length cDNA cloning techniques: cap-trapper technique and oligo-capping technique. Then, we introduced deepCAGE, a cap-trapper and deep sequencing-based TSS profiling technique, and its applications in the research of transcriptional regulation.

关键词: cap-trapper, oligo-capping, deepCAGE, transcription start sites (TSSs), deep sequencing

Abstract: With the accomplishment of the genome draft sequences, identification of functional elements in genome has become an urgent task. Full-length cDNAs provide an important resource for gene identification and their precise structural feature determination. It also provides a basis for genomic element definition. As many regulatory elements are around transcription start sites (TSSs), precise localization of TSSs in the genome becomes a critical step for identifying the associated core promoters. Massive parallel snapshot of TSSs at a particular time under a specific experimental condition makes it possible to globally analyze important regulatory elements around TSSs and further construct transcriptional regulatory networks. In this paper, we first reviewed two important full-length cDNA cloning techniques: cap-trapper technique and oligo-capping technique. Then, we introduced deepCAGE, a cap-trapper and deep sequencing-based TSS profiling technique, and its applications in the research of transcriptional regulation.

Key words: cap-trapper, oligo-capping, deepCAGE, transcription start sites (TSSs), deep sequencing

中图分类号:

Q 291

BAI Ling* (白玲), WANG Qi (王琪), LI Hong-mei (李红梅),CHENG Ming (程酩), ZHANG Ning-bo (. 5-Cap Selection Methods and Their Application in Full-Length cDNA Library Construction and Transcription Start Site Profiling[J]. 上海交通大学学报（英文版）, 2014, 19(5): 580-586.

BAI Ling* (白玲), WANG Qi (王琪), LI Hong-mei (李红梅),CHENG Ming (程酩), ZHANG Ning-bo (张宁波), LI Hua* (李华). 5-Cap Selection Methods and Their Application in Full-Length cDNA Library Construction and Transcription Start Site Profiling[J]. Journal of shanghai Jiaotong University (Science), 2014, 19(5): 580-586.

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5-Cap Selection Methods and Their Application in Full-Length cDNA Library Construction and Transcription Start Site Profiling

5-Cap Selection Methods and Their Application in Full-Length cDNA Library Construction and Transcription Start Site Profiling

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