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5′-Cap selection methods and their application in full-length cDNA library construction and transcription start site profiling

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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.

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Authors and Affiliations

  1. School of Biomedical Engineering, Shanghai Jiaotong University, Shanghai, 200240, China

    Ling Bai  (白 玲), Qi Wang  (王 琪), Hong-mei Li  (李红梅), Ming Cheng  (程 酩), Ning-bo Zhang  (张宁波) & Hua Li  (李 华)

Authors
  1. Ling Bai  (白 玲)
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  2. Qi Wang  (王 琪)
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  3. Hong-mei Li  (李红梅)
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  4. Ming Cheng  (程 酩)
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  5. Ning-bo Zhang  (张宁波)
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  6. Hua Li  (李 华)
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Corresponding authors

Correspondence to Ling Bai  (白 玲) or Hua Li  (李 华).

Additional information

Foundation item: the National Natural Science Foundation of China (Nos. 1137420, 91129000, 21273148, 91229108, 31370750 and 21303104) and the National Basic Research Program (973) of China (No. 2010CB529205)

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Bai, L., Wang, Q., Li, Hm. et al. 5′-Cap selection methods and their application in full-length cDNA library construction and transcription start site profiling. J. Shanghai Jiaotong Univ. (Sci.) 19, 580–586 (2014). https://doi.org/10.1007/s12204-014-1545-z

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  • DOI: https://doi.org/10.1007/s12204-014-1545-z

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