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Genome-Wide Analysis of Long Noncoding RNA Turnover

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Nuclear Bodies and Noncoding RNAs

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1262))

Abstract

Genome-wide analysis for determining RNA turnover is an advanced method in RNA biology that examines the specific half-life of nuclear noncoding RNA (ncRNA). In particular, a pulse-labeling method using uridine analogs enables the determination of RNA stability under physiologically undisturbed conditions. The technique involves pulse labeling of endogenous RNAs in mammalian cells with 5′-bromo-uridine (BrU), followed by measuring the chronological decrease of BrU-labeled RNAs using deep sequencing. The method is called BrU immunoprecipitation chase assay (BRIC) or BRIC through deep sequencing (BRIC-seq). Here, we describe a detailed protocol and technical tips for BRIC-seq.

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Author notes

    Authors and Affiliations

    1. Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan

      Hidenori Tani

    2. Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan

      Naoto Imamachi, Rena Mizutani, Katsutoshi Imamura & Nobuyoshi Akimitsu

    3. Department of Medical and Life Science, Faculty of Pharmaceutical Science, Tokyo University of Science, 2641 Yamazaki, Noda, 278-8510, Japan

      Yeondae Kwon & Satoru Miyazaki

    4. Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8562, Japan

      Sho Maekawa & Yutaka Suzuki

    5. Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8562, Japan

      Yutaka Suzuki

    Authors
    1. Hidenori Tani
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    2. Naoto Imamachi
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    3. Rena Mizutani
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    4. Katsutoshi Imamura
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    5. Yeondae Kwon
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    6. Satoru Miyazaki
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    7. Sho Maekawa
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    8. Yutaka Suzuki
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    9. Nobuyoshi Akimitsu
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    Corresponding author

    Correspondence to Nobuyoshi Akimitsu .

    Editor information

    Editors and Affiliations

    1. RNA Biology Laboratory, RIKEN, Saitama, Japan

      Shinichi Nakagawa

    2. Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan

      Tetsuro Hirose

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    Tani, H. et al. (2015). Genome-Wide Analysis of Long Noncoding RNA Turnover. In: Nakagawa, S., Hirose, T. (eds) Nuclear Bodies and Noncoding RNAs. Methods in Molecular Biology, vol 1262. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2253-6_19

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    • DOI: https://doi.org/10.1007/978-1-4939-2253-6_19

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    • Publisher Name: Humana Press, New York, NY

    • Print ISBN: 978-1-4939-2252-9

    • Online ISBN: 978-1-4939-2253-6

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