Secondary structure-based analysis of mouse brain small RNA sequences obtained by using next-generation sequencing

Hidenori Kiyosawa; Akio Okumura; Saya Okui; Chisato Ushida; Gota Kawai

doi:10.1016/j.ygeno.2015.05.003

Secondary structure-based analysis of mouse brain small RNA sequences obtained by using next-generation sequencing

Genomics. 2015 Aug;106(2):122-8. doi: 10.1016/j.ygeno.2015.05.003. Epub 2015 May 20.

Authors

Hidenori Kiyosawa¹, Akio Okumura², Saya Okui², Chisato Ushida³, Gota Kawai⁴

Affiliations

¹ Department of Environmental Medicine, Kochi Medical School, Kochi University, Oko-cho Kohasu, Nankoku, Kochi 793-8505, Japan. Electronic address: kiyosawa-fks@umin.org.
² Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Tsudanuma, Narashino, Chiba 275-0016, Japan.
³ Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan.
⁴ 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.

PMID: 26003051
DOI: 10.1016/j.ygeno.2015.05.003

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.

Keywords: Next-generation sequencing; Secondary structure-based clustering; Structured non-coding RNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Brain Chemistry*
Cluster Analysis
High-Throughput Nucleotide Sequencing
Male
Mice
Nucleic Acid Conformation
RNA, Small Untranslated / chemistry*
Sequence Analysis, RNA

Substances

RNA, Small Untranslated