title: Discovery and functional analysis of lncRNAs: Methodologies to investigate an uncharacterized transcriptome.
abstract: It is known that more than 70% of mammalian genomes are transcribed, yet the vast majority of transcripts do not code for proteins. Are these noncoding transcripts merely transcriptional noise, or do they serve a biological purpose? Recent developments in genomic analysis technologies, especially sequencing methods, have allowed researchers to create a large atlas of transcriptomes, study subcellular localization, and investigate potential interactions with proteins for a growing number of transcripts. Here, we review the current methodologies available for discovering and investigating functions of long noncoding RNAs (lncRNAs), which require a wide variety of applications to study their potential biological roles. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
authors.affiliation: Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Kaori
authors.initials: K
authors.lastname: Kashi
authors.affiliation: Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Lindsey
authors.initials: L
authors.lastname: Henderson
authors.affiliation: Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Bonetti
authors.affiliation: Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. Electronic address: carninci@riken.jp.
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
mesh_terms: D000818:Animals; D002843:Chromatin / Q000235:genetics; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008322:Mammals; D051379:Mice; D009690:Nucleic Acid Conformation; D062085:RNA, Long Noncoding / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D002843:Chromatin; D062085:RNA, Long Noncoding
keywords: Functional analysis; Genome-wide characterization; Genomics; LncRNA discovery; Next generation sequencing; Noncoding RNA; Secondary structure