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

Abstract

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

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

CLC Number:

Q 291

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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