title: BRIC-seq: a genome-wide approach for determining RNA stability in mammalian cells.
abstract: We recently developed a novel transcriptome analysis method, termed 5'-bromo-uridine (BrU) immunoprecipitation chase-deep sequencing analysis (BRIC-seq). BRIC-seq enables the determination of genome-wide RNA stability by chasing chronological decreases of BrU-labeled RNAs under physiologically undisturbed conditions. The RNA half-life of each transcript is calculated from the decreasing number of BrU-labeled RNA sequence tags measured by deep sequencing of BrU-labeled RNAs. Here, we describe a detailed protocol and provide tips for BRIC-seq, followed by computational analysis.
authors.affiliation: Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
authors.forename: Naoto
authors.initials: N
authors.lastname: Imamachi
authors.affiliation: Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 305-8569, Japan.
authors.forename: Hidenori
authors.initials: H
authors.lastname: Tani
authors.affiliation: Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
authors.forename: Rena
authors.initials: R
authors.lastname: Mizutani
authors.affiliation: The Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Katsutoshi
authors.initials: K
authors.lastname: Imamura
authors.affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan.
authors.forename: Takuma
authors.initials: T
authors.lastname: Irie
authors.affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
authors.affiliation: Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address: akimitsu@ric.u-tokyo.ac.jp.
authors.forename: Nobuyoshi
authors.initials: N
authors.lastname: Akimitsu
mesh_terms: D000818:Animals; D001976:Bromouracil / Q000031:analogs & derivatives; D002874:Chromosome Mapping; D015723:Gene Library; D063990:Gene Ontology; D016678:Genome; D057809:HEK293 Cells; D006207:Half-Life; D006367:HeLa Cells; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020871:RNA Stability; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D013194:Staining and Labeling; D014529:Uridine / Q000031:analogs & derivatives / Q000737:chemistry
chemical_list: D012333:RNA, Messenger; D001976:Bromouracil; C006824:5-bromouridine; D014529:Uridine
keywords: Genome-wide technology; High-throughput sequencing; Massive sequencing analysis; RNA decay; RNA degradation; RNA stability