Genome-Wide Analysis of Long Noncoding RNA Turnover (original) (raw)

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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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 toNobuyoshi Akimitsu .

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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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