title: A novel virtual spectrometry: Visualized regulatory motifs on ADM, rPol{beta} and CD83 mRNAs in human-friendly manners.
abstract: 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 GenoPoemics 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, rPolbeta 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.
authors.affiliation: Takeda Pharmaceutical Company Limited, Wadai, Tsukuba, Ibaraki, Japan. nakamura_shingo@takeda.co.jp
authors.forename: Shingo
authors.initials: S
authors.lastname: Nakamura
mesh_terms: D020121:5' Untranslated Regions; D053607:Adrenomedullin / Q000737:chemistry*; D020816:Amino Acid Motifs; D015703:Antigens, CD / Q000737:chemistry*; D001483:Base Sequence; D019295:Computational Biology; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry*; D006801:Humans; D007136:Immunoglobulins / Q000737:chemistry*; D008562:Membrane Glycoproteins / Q000737:chemistry*; D008969:Molecular Sequence Data; D012333:RNA, Messenger / Q000737:chemistry*; D012984:Software; D013057:Spectrum Analysis; D000097802:CD83 Antigen
chemical_list: D020121:5' Untranslated Regions; D053607:Adrenomedullin; D015703:Antigens, CD; D012321:DNA-Directed RNA Polymerases; D007136:Immunoglobulins; D008562:Membrane Glycoproteins; D012333:RNA, Messenger; D000097802:CD83 Antigen; C105078:RNA polymerase beta subunit