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Identification of a novel leukemic-specific splice variant of DNMT3B and its stability

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Abstract

DNA methyltransferases make use of alternative splicing mechanism to generate various splice variants, but their role(s) in modulating DNA methylation patterns in the cells is unclear. Notably, DNMT3B alone contains nearly 40 different splice variants. In this study, we have identified a novel splice variant of DNMT3B, which lacks exon 7 and 10 from leukemic cell lines which we termed as DNMT3B9. The exon 7 codes for the major part of PWWP domain, and exon 10 inclusion serves as a pluripotent marker. By quantitative RT-PCR using exon–exon junction-specific primers, we showed higher level of DNMT3B9 transcripts in several leukemic cell lines. However, DNMT3B9 expression was less in other tested cancer cell lines indicating that DNMT3B9 might serve as a leukemic-specific biomarker. Surprisingly, endogenous protein for DNMT3B9 was not detected in leukemic cells suggesting the unidentified RNA-related function(s) for DNMT3B9. In addition, we showed that DNMT3B9 protein lacks PWWP domain is less stable compared to other DNMT3B variants which contain PWWP domain through computational predictions and by cycloheximide half-life experiment. Taken together, we demonstrated the existence of novel leukemic-specific splice variant of DNMT3B and provide the evidence for the role of PWWP domain in the stability of DNMT3B. The findings reported here have relevance in epigenetic therapy, which is aimed to target the DNMT3B in cancer cells.

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Acknowledgements

We thank the members of Sudhakar Baluchamy Laboratory for the technical assistance and helpful discussion. We especially thank Dr. Arunkumar Dhayalan for critical reading of the manuscript.

Funding

This study was funded by Science and Engineering Research Board (SERB)—India, and SB/EMEQ-038/2013 to Dr. Sudhakar Baluchamy and Department of Biotechnology (DBT), India, for Prachi Singh and Sarvagalla Sailu fellowship.

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Authors and Affiliations

  1. Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India

    Prachi Singh & Sudhakar Baluchamy

  2. Centre for Bioinformatics, Pondicherry Central University, Pondicherry, 605014, India

    Sarvagalla Sailu & Mohane Selvaraj Coumar

  3. Translational Gerontology Branch, National Institute On Aging, National Institutes of Health, Baltimore, MD, 21224, USA

    Elango Palchamy

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  1. Prachi Singh
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Singh, P., Sailu, S., Palchamy, E. et al. Identification of a novel leukemic-specific splice variant of DNMT3B and its stability. Med Oncol 34, 145 (2017). https://doi.org/10.1007/s12032-017-1008-0

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