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Large conserved domains of low DNA methylation maintained by Dnmt3a

Nature Genetics volume 46, pages 17–23 (2014)Cite this article

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Abstract

Gains and losses in DNA methylation are prominent features of mammalian cell types. To gain insight into the mechanisms that promote shifts in DNA methylation and contribute to changes in cell fate, including malignant transformation, we performed genome-wide mapping of 5-methylcytosine and 5-hydroxymethylcytosine in purified mouse hematopoietic stem cells. We discovered extended regions of low methylation (canyons) that span conserved domains frequently containing transcription factors and are distinct from CpG islands and shores. About half of the genes in these methylation canyons are coated with repressive histone marks, whereas the remainder are covered by activating histone marks and are highly expressed in hematopoietic stem cells (HSCs). Canyon borders are demarked by 5-hydroxymethylcytosine and become eroded in the absence of DNA methyltransferase 3a (Dnmt3a). Genes dysregulated in human leukemias are enriched for canyon-associated genes. The new epigenetic landscape we describe may provide a mechanism for the regulation of hematopoiesis and may contribute to leukemia development.

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Figure 1: Large undermethylated canyons identified by WGBS.
Figure 2: Histone modification and expression of canyon-associated genes.
Figure 3: Erosion of canyon borders in Dnmt3a-null HSCs.
Figure 4: Histone and 5hmC distribution on canyons and cUMRs.
Figure 5: Aberrant expression of canyon-associated genes in hematologic malignancies.

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Acknowledgements

We thank T. Chen, J.P. Issa, J. Gilbert and members of the Goodell laboratory for helpful discussions. This work was supported by US National Institutes of Health (NIH) grants AG036562, CA126752, DK092883, CA125123, DK084259 and AI07495, the Ellison Medical Foundation, Cancer Prevention Research Institute of Texas (CPRIT) grant RP110028 and the Samuel Waxman Foundation (M.A.G.): by CPRIT RP110471, NIH grant RO1HG007538 and DOD PC094421 (W.L.); and by grants CA151535 and CIRM RM1-01729 and Leukemia and Lymphoma Society award 6187-12 (A.R.). Y.H. and M.K. are supported by Leukemia and Lymphoma Society fellowships.

Author information

Author notes

  1. Grant A Challen

    Present address: Present address: Department of Internal Medicine, Washington University at St. Louis, St. Louis, Missouri, USA.,

  2. Mira Jeong, Deqiang Sun and Min Luo: These authors contributed equally to this work.

  3. Wei Li and Margaret A Goodell: These authors jointly directed this work.

Authors and Affiliations

  1. Department of Pediatrics and Molecular & Human Genetics, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas, USA

    Mira Jeong, Min Luo, Grant A Challen, Xiaotian Zhang, Liubin Yang & Margaret A Goodell

  2. Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA

    Deqiang Sun, Benjamin Rodriguez & Wei Li

  3. Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA

    Yun Huang, Lukas Chavez, Myunggon Ko & Anjana Rao

  4. Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA

    Hui Wang & Rui Chen

  5. Department of Hematology, Cambridge Institute for Medical Research and Wellcome Trust and Medical Research Council Cambridge Stem Cell Institute, Cambridge University, Cambridge, UK

    Rebecca Hannah & Berthold Göttgens

  6. Department of Systems Biology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA

    Sang-Bae Kim & Ju-Seog Lee

  7. Department of Pathology, Baylor College of Medicine, Houston, Texas, USA

    Preethi Gunaratne

  8. Department of Biology & Biochemistry, University of Houston, Houston, Texas, USA

    Preethi Gunaratne

  9. Department of Medicine, University of Chicago, Chicago, Illinois, USA

    Lucy A Godley

  10. Huffington Center for Aging, Baylor College of Medicine, Houston, Texas, USA

    Gretchen J Darlington

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Contributions

M.J., M.L., G.A.C., X.Z., Y.H., M.K., H.W., L.Y. and R.C. designed and performed experiments. M.J., D.S., M.L., G.A.C., B.R., L.C., S.-B.K., R.H., L.A.G., A.R., G.J.D., W.L. and M.A.G. analyzed data. M.J., D.S., M.L., G.A.C., B.R., J.-S.L., B.G., P.G., L.A.G., G.J.D., A.R., W.L. and M.A.G. wrote and edited the manuscript.

Corresponding authors

Correspondence to Wei Li or Margaret A Goodell.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–12 (PDF 2094 kb)

Supplementary Table 1

Whole-genome sequencing statistics (XLSX 12 kb)

Supplementary Table 2

UMRs in WT HSCs (XLSX 3111 kb)

Supplementary Table 3

UMRs in HOX genes (XLSX 42 kb)

Supplementary Table 4

UMRs in ESCs (XLSX 1819 kb)

Supplementary Table 5

Canyons versus UMRs (XLSX 13 kb)

Supplementary Table 6

WT versus Dnmt3a KO HSC UMRs (XLSX 9021 kb)

Supplementary Table 7

5hmC sites in WT and Dnmt3a KO (XLSX 21506 kb)

Supplementary Table 8

oxBS sequencing (XLSX 21 kb)

Supplementary Table 9

Summary of genes overlapping leukemia Oncomine signatures (XLSX 246 kb)

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Jeong, M., Sun, D., Luo, M. et al. Large conserved domains of low DNA methylation maintained by Dnmt3a. Nat Genet 46, 17–23 (2014). https://doi.org/10.1038/ng.2836

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