Abstract

DNA methylation was first described almost a century ago; however, the rules governing its establishment and maintenance remain elusive. Here we present data demonstrating that active transcription regulates levels of genomic methylation. We identify a novel RNA arising from the CEBPA gene locus that is critical in regulating the local DNA methylation profile. This RNA binds to DNMT1 and prevents CEBPA gene locus methylation. Deep sequencing of transcripts associated with DNMT1 combined with genome-scale methylation and expression profiling extend the generality of this finding to numerous gene loci. Collectively, these results delineate the nature of DNMT1–RNA interactions and suggest strategies for gene-selective demethylation of therapeutic targets in human diseases.

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Accessions

Data deposits

Sequencing and microarray data sets are available for download at Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/projects/geo/) under the following accession numbers: microarray expression, GSE32153; RIPseq, GSE32162; RRBS, GSE32168; and RNAseq, GSE41279. The accession number for the project is GSE32260.

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Acknowledgements

This work was supported by grants CA118316, CA66996 and HL56745 from the National Institutes of Health (NIH) to D.G.T., the Italian Foundation for Cancer Research (FIRC) ‘Leonino Fontana e Maria Lionello’ fellowship, the NIH T32 HL007917-11A1 and the Società Italiana di Ematologia Sperimentale (SIES) ‘Dr.Tito Bastianello’ fellowship to A.D.R.; FAMRI CIA (103063) grant to A.K.E.; Fondazione Roma ‘Progetto cellule staminali’ to G.L. and F.D’A.; the American Italian Cancer Foundation Fellowship (AICF) to G.A.; Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)—grant no. 2011/11822-6—to L.L.D.F.P.; the National Research Foundation and the Singapore Ministry of Education under its Centres of Excellence initiative to M.W. and T.B.; the MSMT Navrat grant LK21307 to M.A.-J. S.P. and J.T. were supported by New England Biolabs. We thank R. White, D. Johnson, M. Frank-Kamenetskii, S. M. Mirkin, D. Gautheret, B. Tazon-Vega, C. Bonifer, C. Bock, M. T. Voso, J. J. Dunn (deceased) and R. A. M. Fouchier for helpful advice and reagents; I. Rigoutsos for providing the latest released pyknons database; all the members of the Tenen Laboratory; P. Tan and T. S. Ting from the Genome Institute of Singapore; R. Soong from the Cancer Science Institute Translational Interface; J. LaVecchio and G. Buruzula from the Harvard Stem Cell Institute/Joslin Diabetes Center flow cytometry facility; and F. Hyde from Epicentre-Illumina. This research is supported by the Singapore Ministry of Health’s National Medical Research Council under its Singapore Translational Research (STaR) Investigator Award (D.G.T.).

Author information

Author notes

    • Annalisa Di Ruscio
    •  & Alexander K. Ebralidze

    These authors contributed equally to this work.

Affiliations

  1. Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Annalisa Di Ruscio
    • , Alexander K. Ebralidze
    • , Giovanni Amabile
    • , Lorena Lobo De Figueiredo Pontes
    • , Meritxell Alberich-Jorda
    • , Pu Zhang
    • , John L. Rinn
    •  & Daniel G. Tenen
  2. Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA

    • Annalisa Di Ruscio
    • , Alexander K. Ebralidze
    • , Giovanni Amabile
    • , Lorena Lobo De Figueiredo Pontes
    • , Meritxell Alberich-Jorda
    • , Konstantin K. Ebralidze
    •  & John L. Rinn
  3. Università Cattolica del Sacro Cuore, Institute of Hematology, L.go A. Gemelli 8, Rome 00168, Italy

    • Annalisa Di Ruscio
    • , Francesco D’Alò
    •  & Giuseppe Leone
  4. Cancer Science Institute, National University of Singapore, 117599, Singapore

    • Touati Benoukraf
    • , Mengchu Wu
    •  & Daniel G. Tenen
  5. Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA

    • Loyal A. Goff
    •  & John L. Rinn
  6. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA

    • Loyal A. Goff
    •  & John L. Rinn
  7. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, Massachusetts 02139, USA

    • Loyal A. Goff
  8. New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938-2723, USA

    • Jolyon Terragni
    •  & Sriharsa Pradhan
  9. University of Michigan, Department of Pathology, Ann Arbor, Michigan 48109-2200, USA

    • Maria Eugenia Figueroa
  10. Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic

    • Meritxell Alberich-Jorda
  11. Department of Medicine, Hematology-Oncology, C-620 Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, USA

    • Ari Melnick

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Contributions

D.G.T. supervised the project; A.D.R., A.K.E. and D.G.T. conceived and designed the study; A.D.R., A.K.E., G.A., P.Z., M.A.-J., F.D’A., S.P., L.L.D.F.P. and J.T. performed experiments; M.W. performed sequencing and microarray experiments; T.B. and L.A.G. analysed RIP-seq, RNA-seq, RRBS and microarray data; M.E.F. and A.M. performed the MassARRAY experiment and assisted in the analysis; A.D.R., A.K.E., G.L., K.K.E., J.L.R. and D.G.T. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Daniel G. Tenen.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Results, Supplementary Methods, Supplementary References and Supplementary Figures 1-6.

Excel files

  1. 1.

    Supplementary Data 1

    This file contains the MassARRAY primer sets.

  2. 2.

    Supplementary Data 2

    This file contains a list of gene loci belonging to DNMT1-bound and unbound groups along with respective expression and DNA methylation levels.

  3. 3.

    Supplementary Data 3

    This file contains a full list of Biological Process Gene Ontology terms significantly enriched in cluster C.

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DOI

https://doi.org/10.1038/nature12598

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