Journal of Biochemistry Advance Access originally published online on April 22, 2009
Journal of Biochemistry 2009 146(2):251-261; doi:10.1093/jb/mvp064
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A Novel Virtual Spectrometry: Visualized Regulatory Motifs on ADM, rPolβ and CD83 mRNAs in Human-friendly Manners
Frontier Research Laboratories, Takeda Pharmaceutical Company Limited, 10 Wadai, Tsukuba, Ibaraki 300-4293, Japan
*To whom correspondence should be addressed. Tel: +81-29-864-5034, Fax: +81-29-864-5000, E-mail: nakamura_shingo{at}takeda.co.jp
Received March 23, 2009; Accepted April 6, 2009
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Abstract |
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Recently, riboswitches and other structures discovered on mRNAs have been reported as examples of functional RNA structures, motifs. Such motifs were shown to be present as single-form valid structures but they are obscured among other less-valid structures. Here, I present a novel, practical virtual spectrometry (the GenoPoemicsTM Spectrometry) visualizing motifs on mRNA strands as spectra at-a-glance. Every motif along with validity of their existences could be observed on the spectra in human-friendly manners, and whole structures of mRNAs could be overviewed. Therefore, the spectra helped distinguish valid and less valid motifs. The spectrometry was applied to variety of mRNAs such as ADM, rPolβ and CD83 to identify structures of high validity on them, previously reported functional motifs were successfully revealed. These findings indicate that the structures of mRNAs that may be folded into multiple forms can be further discussed quantitatively based on the visual spectra to discover functional RNA motifs.
Key Words: mRNA structure, Maxwell-Boltzmann distribution, virtual spectrometry motifs, regulatory motifs, protein binding motifs