Brief Communication

Nm-seq maps 2′-O-methylation sites in human mRNA with base precision

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Abstract

The ribose of RNA nucleotides can be 2′-O-methylated (Nm). Despite advances in high-throughput detection, the inert chemical nature of Nm still limits sensitivity and precludes mapping in mRNA. We leveraged the differential reactivity of 2′-O-methylated and 2′-hydroxylated nucleosides to periodate oxidation to develop Nm-seq, a sensitive method for transcriptome-wide mapping of Nm with base precision. Nm-seq uncovered thousands of Nm sites in human mRNA with features suggesting functional roles.

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Acknowledgements

This work was supported by the US National Institutes of Health NHGRI RM1 HG008935 to C.H.; a grant from the Kahn Family Foundation to D.D. and G.R.; and grants from the Ernest and Bonnie Beutler Research Program, Flight Attendant Medical Research Institute (FAMRI) and the Israeli Centers of Excellence (I-CORE) Program (ISF grants no. 41/11 and no. 1796/12) to G.R. C.H. is an investigator of the Howard Hughes Medical Institute (HHMI). G.R. is a member of the Sagol Neuroscience Network and holds the Djerassi Chair for Oncology at the Sackler Faculty of Medicine, Tel-Aviv University, Israel. D.D. was supported by a Human Frontier Science Program (HFSP) long-term fellowship. Q.D. is supported by the National Institutes of Health grant K01 HG006699. We wish to thank M. Salmon-Divon for advice and help with bioinformatic analysis and R. Mashiach for help with chemical structure drawings.

Author information

Author notes

    • Qing Dai
    • , Sharon Moshitch-Moshkovitz
    •  & Dali Han

    These authors contributed equally to this work.

    • Dan Dominissini
    •  & Chuan He

    These authors jointly supervised this work.

Affiliations

  1. Department of Chemistry, The University of Chicago, Chicago, Illinois, USA.

    • Qing Dai
    • , Dali Han
    •  & Chuan He
  2. Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois, USA.

    • Qing Dai
    • , Dali Han
    •  & Chuan He
  3. Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel.

    • Sharon Moshitch-Moshkovitz
    • , Nitzan Kol
    • , Ninette Amariglio
    • , Gideon Rechavi
    •  & Dan Dominissini
  4. Wohl Centre for Translational Medicine, Chaim Sheba Medical Center, Tel-Hashomer, Israel.

    • Sharon Moshitch-Moshkovitz
    • , Ninette Amariglio
    • , Gideon Rechavi
    •  & Dan Dominissini
  5. The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.

    • Ninette Amariglio
  6. Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.

    • Gideon Rechavi
    •  & Dan Dominissini
  7. Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA.

    • Chuan He
  8. Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA.

    • Chuan He

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Contributions

D.D., Q.D. and C.H. conceived the approach. D.D. and Q.D. developed the methods and performed experiments. D.D., S.M.-M., D.H. and N.K. analyzed the data. D.D., S.M.-M., N.A., G.R. and C.H. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Dan Dominissini or Chuan He.

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