Journal of Neuro-Oncology

, Volume 104, Issue 2, pp 483–494 | Cite as

Epigenetic regulation of DNA methyltransferases: DNMT1 and DNMT3B in gliomas

  • Ganeshkumar Rajendran
  • Karthik Shanmuganandam
  • Ameya Bendre
  • Dattatreya Mujumdar
  • Abhay Goel
  • Anjali Shiras
Laboratory Investigation - Human/Animal Tissue


The role of epigenetics and significance of aberrant gene regulation in etiology of cancer is a well-established phenomenon. The hallmark of cancer epigenetics is aberrant DNA methylation consisting of global hypomethylation and regional hypermethylation of tumor suppressor genes (TSGs) by DNA methyltransferases (DNMTs). In mammals, DNA methylation is catalyzed by DNMTs encoded by DNMT1, DNMT3A, and DNMT3B. Interestingly, little is known about variation in the methylation status of epigenetic regulators themselves in gliomas. Here, we report significant overexpression of DNMT1 and DNMT3B. A study of the methylation status and histone modifications at the promoter region of DNA methyltransferase I (DNMT1) gene revealed an unmethylated DNA promoter, similar to that detected in normal brain tissues. However, a differential histone code with distinct euchromatin marks—AcH3, AcH4, and H3k4me2—was specifically detected in tumors, unlike in normal brain tissues, which were found predominantly enriched with heterochromatin marks such as H3K9me2 and H3K27me3. In contrast, a differential methylation pattern of DNMT3B gene promoter occurred in glioma tumors, wherein it was found hypomethylated. Transcriptional silencing by CpG island methylation is a prevalent mechanism for inactivation of TSGs. Inhibiting DNMTs by 5-azacytidine (DNMT inhibitor) treatment led to significant inhibition of expression of DNMT1 and DNMT3B and enhanced expression of TSGs such as PTEN and p21 analyzed in this study. Our studies have identified effects of increased presence of DNMTs on inhibition of tumor suppressors that are epigenetically silenced in gliomas, thereby leading to aberrant regulation of cell cycle progression and failure to maintain genomic stability.


Tumor suppressor genes Histone modifications Acetylation DNA methylation MS-PCR ChIP assay 



We gratefully acknowledge the financial support of the Department of Biotechnology, Government of India in this study. The fellowship of K.S. was supported through project funding from the Department of Biotechnology (DBT), Government of India. Gk.R. was supported by a fellowship from the Council for Scientific and Industrial Research (CSIR), Government of India. We acknowledge the expertise of Mr. Sachin Rathod and Mr. Aman Sharma in establishment of long-term cultures from tumor and normal tissues.

Supplementary material

11060_2010_520_MOESM1_ESM.tif (1.1 mb)
Fig. S1 q-RT-PCR expression of DNMT3B over DNMT1. (A) Low- and (B) high-grade gliomas. All samples were run in triplicate and normalized with respect to human Gapdh controls. Expression of DNMT1 and DNMT3B genes was normalized with respect to NBT1, NBT2, and NBT3. Values represent mean ± SD (n = 3) (TIFF 1095 kb)
11060_2010_520_MOESM2_ESM.tif (223 kb)
Fig. S2 qRT-PCR analyses for validation of ChIP data. In reactions where a faint PCR product was obtained in nonspecific IgG lanes, q-PCR was performed to ensure specificity and subtracted with nonspecific IgG. (A) Acetylated histone H3 in LN18, (B) dimethylation of histone H3 lysine 4 in LN18, and (C) acetylated histone H3 in U87MG (TIFF 223 kb)


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Copyright information

© Springer Science+Business Media, LLC. 2011

Authors and Affiliations

  • Ganeshkumar Rajendran
    • 1
  • Karthik Shanmuganandam
    • 1
  • Ameya Bendre
    • 1
  • Dattatreya Mujumdar
    • 2
  • Abhay Goel
    • 2
  • Anjali Shiras
    • 1
  1. 1.National Centre for Cell Science (NCCS)PuneIndia
  2. 2.Seth GS Medical College and KEM HospitalMumbaiIndia

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