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Bisulfite-free mapping of DNA cytosine modifications: challenges and perspectives

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Abstract

The mapping of DNA cytosine modifications is crucial for understanding the dynamic landscape of epigenetic regulation. While bisulfite sequencing has been the gold standard for decades, it suffers from limitations such as DNA degradation and low library quality due to harsh chemical treatment. In recent years, bisulfite-free methods have emerged as promising alternatives for detecting and quantifying DNA cytosine modifications. These methods employ enzymatic and chemical strategies to investigate cytosine modifications without the need for bisulfite treatment. This review provides an overview of the historical context of bisulfite-based methods and presents the current landscape of bisulfite-free methods. The advantages and limitations of each approach are discussed, along with insights into their applications. Furthermore, the review explores the existing challenges in the field and presents future perspectives and potential directions for advancing bisulfite-free mapping methods. The continued progress in bisulfite-free techniques holds great promise for unraveling the intricate nature of DNA cytosine modifications and their functional implications in diverse biological processes and diseases.

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Acknowledgements This work was supported by the start-up funding from Wuhan University and Fundamental Research Funds for the Central Universities (2042023kf0118).

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  1. College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China

    Yanfang Du, Ying Tang, Bingqian Lin, Xiaochen Xue & Yibin Liu

  2. School of Public Health, Wuhan University, Wuhan, 430071, China

    Yafen Wang

  3. Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China

    Yibin Liu

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  1. Yanfang Du
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Du, Y., Tang, Y., Lin, B. et al. Bisulfite-free mapping of DNA cytosine modifications: challenges and perspectives. Sci. China Chem. 66, 3044–3053 (2023). https://doi.org/10.1007/s11426-023-1729-2

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