title: Secondary structure-based analysis of mouse brain small RNA sequences obtained by using next-generation sequencing.
abstract: In order to find novel structured small RNAs, next-generation sequencing was applied to small RNA fractions with lengths ranging from 40 to 140 nt and secondary structure-based clustering was performed. Sequences of structured RNAs were effectively clustered and analyzed by secondary structure. Although more than 99% of the obtained sequences were known RNAs, 16 candidate mouse structured small non-coding RNAs (MsncRs) were isolated. Based on these results, the merits of secondary structure-based analysis are discussed.
authors.affiliation: Department of Environmental Medicine, Kochi Medical School, Kochi University, Oko-cho Kohasu, Nankoku, Kochi 793-8505, Japan. Electronic address: kiyosawa-fks@umin.org.
authors.forename: Hidenori
authors.initials: H
authors.lastname: Kiyosawa
authors.affiliation: Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Tsudanuma, Narashino, Chiba 275-0016, Japan.
authors.forename: Akio
authors.initials: A
authors.lastname: Okumura
authors.affiliation: Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Tsudanuma, Narashino, Chiba 275-0016, Japan.
authors.forename: Saya
authors.initials: S
authors.lastname: Okui
authors.affiliation: Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan.
authors.forename: Chisato
authors.initials: C
authors.lastname: Ushida
authors.affiliation: Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Tsudanuma, Narashino, Chiba 275-0016, Japan. Electronic address: gkawai@sea.it-chiba.ac.jp.
authors.forename: Gota
authors.initials: G
authors.lastname: Kawai
mesh_terms: D000818:Animals; D001923:Brain Chemistry; D016000:Cluster Analysis; D059014:High-Throughput Nucleotide Sequencing; D008297:Male; D051379:Mice; D009690:Nucleic Acid Conformation; D058727:RNA, Small Untranslated / Q000737:chemistry*; D017423:Sequence Analysis, RNA
chemical_list: D058727:RNA, Small Untranslated
keywords: Next-generation sequencing; Secondary structure-based clustering; Structured non-coding RNA