Advertisement

Transcriptome-Wide Mapping 5-Methylcytosine by m5C RNA Immunoprecipitation Followed by Deep Sequencing in Plant

  • Xiaofeng GuEmail author
  • Zhe Liang
Part of the Methods in Molecular Biology book series (MIMB, volume 1933)

Abstract

Transcriptome-wide mapping RNA modification is crucial to understand the distribution and function of RNA modifications. Here, we describe a protocol to transcriptome-wide mapping 5-methylcytosine (m5C) in plant, by a RNA immunoprecipitation followed by deep sequencing (m5C-RIP-seq) approach. The procedure includes RNA extraction, fragmentation, RNA immunoprecipitation, and library construction.

Key words

RNA methylation 5-Methylcytosine m5m5C-RIP-seq RNA immunoprecipitation Plant 

Notes

Acknowledgments

This work was supported by Ministry of Science and Technology of the People’s Republic of China (2016YFD0101001) to X.G., National Natural Science Foundation of China (31671670) to X.G., and Recruitment program of Global Youth Expert of China to X.G.

References

  1. 1.
    Machnicka MA, Milanowska K, Osman O et al (2013) MODOMICS: a database of RNA modification pathways—2013 update. Nucleic Acids Res 41:262–267CrossRefGoogle Scholar
  2. 2.
    Zhao BS, Roundtree IA, He C (2017) Post-transcriptional gene regulation by mRNA modifications. Nat Rev Mol Cell Biol 18(1):31–42CrossRefGoogle Scholar
  3. 3.
    Gilbert WV, Bell TA, Schaening C (2016) Messenger RNA modifications: form, distribution, and function. Science 352(6292):1408–1412CrossRefGoogle Scholar
  4. 4.
    Shen LS, Liang Z, Gu XF et al (2016) N6-Methyladenosine RNA modification regulates shoot stem cell fate in Arabidopsis. Dev Cell 38(2):186–200CrossRefGoogle Scholar
  5. 5.
    Dominissini D, Moshitch-Moshkovitz S, Salmon-Divon M, Amariglio N, Rechavi G (2013) Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing. Nat Protoc 8(1):176–189CrossRefGoogle Scholar
  6. 6.
    Cui XA, Liang Z, Shen LS et al (2017) 5-Methylcytosine RNA methylation in Arabidopsis thaliana. Mol Plant 10(11):1387–1399CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijingChina
  2. 2.Department of Biological SciencesNational University of SingaporeSingaporeSingapore

Personalised recommendations