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DNA Research Advance Access published online on May 16, 2008
DNA Research, doi:10.1093/dnares/dsn010
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© The Author 2008. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Fine Expression Profiling of Full-length Transcripts using a Size-unbiased cDNA Library Prepared with the Vector-capping Method

Mio Oshikawa1,2, Yoshiko Sugai1,2, Ron Usami2, Kuniyo Ohtoko1, Shigeru Toyama1 and Seishi Kato1,*

1 Department of Rehabilitation Engineering, Research Institute, National Rehabilitation Center for Persons with Disabilities, 4-1 Namiki, Tokorozawa, Saitama 359-8555, Japan
2 Department of Biological Applied Chemistry, Graduate School of Engineering, Toyo University, Kujirai 2100, Kawagoe, Saitama 350-8585, Japan

Received 24 December 2007 ; accepted 10 April 2008.

Recently, we have developed a vector-capping method for constructing a full-length cDNA library. In the present study, we performed in-depth analysis of the vector-capped cDNA library prepared from a single type of cell. As a result of single-pass sequencing analysis of 24 000 clones randomly isolated from the unamplified library, we identified 19 951 full-length cDNA clones whose intactness was confirmed by the presence of an additional G at their 5' end. The full-length cDNA content was >95%. Mapping these sequences to the human genome, we identified 4513 transcriptional units that include 36 antisense transcripts against known genes. Comparison of the frequencies of abundant clones showed that the expression profiles of different libraries, including the distribution of transcriptional start sites (TSSs), were reproducible. The analysis of long-sized cDNAs showed that this library contained many cDNAs with a long-sized insert up to 11 199 bp of golgin B, including multiple slicing variants for filamin A and filamin B. These results suggest that the size-unbiased full-length cDNA library constructed using the vector-capping method will be an ideal resource for fine expression profiling of transcriptional variants with alternative TSSs and alternative splicing.

Key words: full-length cDNA; expression profile; transcriptional start site; alternative splicing; antisense transcript

* To whom correspondence should be addressed. Tel. +81 4-2995-3100. Fax. +81 4-2995-3132. E-mail: seishi{at}rehab.go.jp

Edited by Minoru Ko


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