A RecA-mediated exon profiling method

Yuki Hasegawa, Shiro Fukuda, Kazuro Shimokawa, Shinji Kondo, Norihiro Maeda, Yoshihide Hayashizaki

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

We have developed a RecA-mediated simple, rapid and scalable method for identifying novel alternatively spliced full-length cDNA candidates. This method is based on the principle that RecA proteins allow to carry radioisotope-labeled probe DNAs to their homologous sequences, resulting in forming triplexes. The resulting complex is easily detected by mobility difference on electrophoresis. We applied this exon profiling method to four selected mouse genes as a feasibility study. To design probes for detection, the information on known exonic regions was extracted from public database, RefSeq. Concerning the potentially transcribed novel exonic regions, RNA mapping experiment using Affymetrix tiling array was performed. As a result, we were able to identify alternative splice variants of Thioredoxin domain containing 5, Interleukin1β, Interleukin 1 family 6 and glutamine-rich hypothetical protein. In addition, full-length sequencing demonstrated that our method could profile exon structures with >90% accuracy. This reliable method can allow us to screen novel splice variants from a huge number of cDNA clone set effectively.

Original languageEnglish
Article numbere97
JournalNucleic acids research
Volume34
Issue number13
DOIs
Publication statusPublished - 2006 Sep 22
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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    Hasegawa, Y., Fukuda, S., Shimokawa, K., Kondo, S., Maeda, N., & Hayashizaki, Y. (2006). A RecA-mediated exon profiling method. Nucleic acids research, 34(13), [e97]. https://doi.org/10.1093/nar/gkl497