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Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3

Nature Genetics volume 37, pages 645–651 (2005)Cite this article

Abstract

CpG islands are present in one-half of all human and mouse genes and typically overlap with promoters or exons. We developed a method for high-resolution analysis of the methylation status of CpG islands genome-wide, using arrays of BAC clones and the methylation-sensitive restriction enzyme NotI. Here we demonstrate the accuracy and specificity of the method. By computationally mapping all NotI sites, methylation events can be defined with single-nucleotide precision throughout the genome. We also demonstrate the unique expandability of the array method using a different methylation-sensitive restriction enzyme, BssHII. We identified and validated new CpG island loci that are methylated in a tissue-specific manner in normal human tissues. The methylation status of the CpG islands is associated with gene expression for several genes, including SHANK3, which encodes a structural protein in neuronal postsynaptic densities. Defects in SHANK3 seem to underlie human 22q13 deletion syndrome. Furthermore, these patterns for SHANK3 are conserved in mice and rats.

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Figure 1: Detection of methylation differences using a BAC clone array.
Figure 2: The log2 ratios of cohybridizations of NotI fragments did not have either intensity-dependent effects or geographic location-specific effects.
Figure 3: Detection of methylation differences between cell types using NotI or BssHII.
Figure 4: Validation of the array results by bisulfite-sequencing and gene-expression analysis.
Figure 5: Evolutionary conservation of tissue-specific CpG island methylation and gene expression in SHANK3.

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Acknowledgements

We thank J. Nakamura for providing rat tissues. This work was supported by the California Breast Cancer Research Program (T.T.C.), Howard Hughes Medical Institute (P.J.), American Brain Tumor Association (C.H.) and US National Institutes of Health (J.F.C.).

Author information

Author notes

  1. Tsui-Ting Ching and Alika K Maunakea: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Neurological Surgery and the Biomedical Sciences Program, The Brain Tumor Research Center, University of California San Francisco, San Franciso, 94143, California, USA

    Tsui-Ting Ching, Alika K Maunakea, Peter Jun, Chibo Hong, Giuseppe Zardo & Joseph F Costello

  2. Department of Laboratory Medicine, University of California San Francisco, San Franciso, 94143, California, USA

    Daniel Pinkel

  3. Cancer Research Institute, University of California San Francisco, San Franciso, 94143, California, USA

    Donna G Albertson, Jian-Hua Mao & Ksenya Shchors

  4. Department of Epidemiology and Biostatistics, University of California San Francisco, San Franciso, 94143, California, USA

    Jane Fridlyand

  5. Department of Neurology, University of California San Francisco, San Franciso, 94143, California, USA

    William A Weiss

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Correspondence to Joseph F Costello.

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Supplementary information

Supplementary Fig. 1

The log2 ratios of cohybridizations of BssHII fragments do not exhibit intensity-dependent effects nor geographic location-specific effects. (PDF 238 kb)

Supplementary Fig. 2

Maps of the chromosomal loci corresponding to BAC clones and their loci that exhibit tissue-specific methylation. (PDF 61 kb)

Supplementary Fig. 3

The tissue-specific CpG island methylation and gene expression of SHANK3 is conserved in rat brain and PBL. (PDF 84 kb)

Supplementary Table 1

Primer sequences and cycling conditions. (PDF 22 kb)

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Ching, TT., Maunakea, A., Jun, P. et al. Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3. Nat Genet 37, 645–651 (2005). https://doi.org/10.1038/ng1563

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