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A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases

Nature Structural & Molecular Biology volume 15, pages 268–279 (2008)Cite this article

A Corrigendum to this article was published on 01 September 2008

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Abstract

Dicer initiates RNA interference by generating small RNAs involved in various silencing pathways. Dicer participates in centromeric silencing, but its role in the epigenetic regulation of other chromatin domains has not been explored. Here we show that Dicer1 deficiency in Mus musculus leads to decreased DNA methylation, concomitant with increased telomere recombination and telomere elongation. These DNA-methylation defects correlate with decreased expression of Dnmt1, Dnmt3a and Dnmt3b DNA methyltransferases (Dnmts), and methylation levels can be recovered by their overexpression. We identify the retinoblastoma-like 2 protein (Rbl2) as responsible for decreased Dnmt expression in Dicer1-null cells, suggesting the existence of Dicer-dependent small RNAs that target Rbl2. We identify the miR-290 cluster as being downregulated in Dicer1-deficient cells and show that it silences Rbl2, thereby controlling Dnmt expression. These results identify a pathway by which miR-290 directly regulates Rbl2-dependent Dnmt expression, indirectly affecting telomere-length homeostasis.

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Figure 1: Defective DNA methylation in Dicer1-null cells.
Figure 2: Defective DNA methylation of Dicer1-null cells.
Figure 3: Increased telomere recombination and aberrantly elongated telomeres in Dicer1-null cells.
Figure 4: Decreased telomerase activity and normal expression of telomere-binding proteins in the absence of Dicer.
Figure 5: Dicer is not required to direct heterochromatic histone marks and HP1 binding at mammalian telomeres and subtelomeres.
Figure 6: Increased expression of Retinoblastoma (Rb) family proteins in Dicer1-null cells is responsible of the decreased expression of Dnmt1, Dnmt3a and Dnmt3b.
Figure 7: The miR-290 cluster targets Rbl2 and controls Dnmt3a,3b expression.
Figure 8: A previously unknown miR-290–dependent pathway controls DNA methylation via Rbl2 and affects telomere integrity and telomere-length homeostasis.

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  • 18 June 2008

    In the version of this article initially published, the GEO accession number for the array data was not provided. It is GSE11229. The error has been corrected in the HTML and PDF versions of the article.

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Acknowledgements

We are indebted to O. Dominguez and D. Pisano from the Genomics and Bioinformatics Units of the Spanish National Cancer Centre (CNIO), respectively, for help with bisulfite sequencing analysis and various microarray and genome-sequence analyses. R.B. is a staff investigator of the CNIO, S.G. is a Fondo de Investigaciones Sanitarias (FIS) senior scientist. P.M. is a 'Ramon y Cajal' senior scientist. I.J. is a student of the Gulbenkian Ph.D. Program in Biomedicine, supported by FCT/MCT (Portugal). M.A.B.'s laboratory is funded by the MCyT (SAF2005-00277, GEN2001-4856-C13-08), by the Regional Government of Madrid (GR/SAL/0597/2004), European Union (TELOSENS FIGH-CT-2002-00217, INTACT LSHC-CT-2003-506803, ZINCAGE FOOD-CT-2003-506850, RISC-RAD FI6R-CT-2003-508842, MOL CANCER MED LSHC-CT-2004-502943) and the Josef Steiner Cancer Research Award, 2003.

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Authors and Affiliations

  1. Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), 3 Melchor Fernández Almagro, Madrid, E-28029, Spain

    Roberta Benetti, Susana Gonzalo, Isabel Jaco, Purificación Muñoz, Stefan Schoeftner, Peter Klatt & Maria A Blasco

  2. Radiation and Cancer Biology Division, Department of Radiation Oncology, Washington University School of Medicine, 4511 Forest Park, 3rd Floor, St. Louis, 63108, Missouri, USA

    Susana Gonzalo

  3. Tumor Suppression Group, Molecular Oncology Program, CNIO, 3 Melchor Fernández Almagro, Madrid, E-28029, Spain

    Susana Gonzalez & Manuel Serrano

  4. Cold Spring Harbor Laboratory, Cold Spring Harbor, 1 Bungtown Road, New York, 11724, USA

    Elizabeth Murchison & Gregory Hannon

  5. Department of Dermatology, University of Pennsylvania, M8D Stellar-Chance Laboratories, 422 Curie Boulevard, Philadelphia, 19104-6100, Pennsylvania, USA

    Thomas Andl & Sarah Millar

  6. Epigenetics Program, Novartis Institutes for Biomedical Research, USCA, 600-5C-146, 250 Massachusetts Avenue, Cambridge, 02139, Massachusetts, USA

    Taiping Chen & En Li

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  1. Roberta Benetti
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Contributions

R.B. performed experiments shown in all manuscript figures as well as designed the experiments together with M.A.B. and S. Gonzalo. S. Gonzalo performed part of the experiments shown in Figure 3c,d and Figure 5. I.J. performed some of the experiments shown in Figure 3a,b. P.M. performed the experiments shown in Figure 3e,f. S. Gonzalez and M.S. generated the miRNA data shown in Figure 7a. S.S. contributed to initial characterization of Dicer1-null telomeric chromatin. E.M. and G.H. provided the Dicer1-null cells and helped with the writing of the manuscript. T.A. and S.M. provided the Dicer1-null skin samples. T.C. and E.L. provided the Dnmt-deficient cells and the Dnmt constructs. P.K. and M.A.B. prepared the manuscript figures. M.A.B., R.B. and S. Gonzalo wrote the paper.

Corresponding author

Correspondence to Maria A Blasco.

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Benetti, R., Gonzalo, S., Jaco, I. et al. A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases. Nat Struct Mol Biol 15, 268–279 (2008). https://doi.org/10.1038/nsmb.1399

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