Chemical-based sequencing method to efficiently study DNA methylation

One way cells can control the activities of their genes is by adding small chemical modifications to DNA that control which genes are turned on or off. Methyl groups are one of these chemical modifications or tags. Researchers have found that in bacteria, DNA methylation plays a role in regulating virulence, reproduction and gene expression. In other organisms, including humans, DNA methylation is essential in regulating tissue-specific gene expression, which defines the nature of a cell, for example whether it is a skin cell or a brain cell.

The study of DNA methylation is part of the field of epigenetics. It’s important because it helps us understand why one type of bacteria causes more serious disease than another or how a normal cell can change and cause disease, such as cancer.”


dr. Tao Wu, corresponding author, assistant professor of molecular and human genetics at Baylor College of Medicine

The Wu Lab is an epigenetic laboratory for cancer. The long-term goal is to overcome the therapeutic resistance of cancer by better understanding the role of epigenetics in this disease.

In bacteria, there are three different forms of DNA methylation. The most common is one that tags the DNA base or building block adenine (N6-methyladenine or 6mA). The other two tag the DNA base cytosine (N4-methylcytosine or 4mC and 5-methylcytosine or 5mC). While there are many methods to study DNA methylation, a few can efficiently map the three types simultaneously, Wu explained.

“It was thought that organisms other than bacteria, including mammals, usually only use methyl-cytosine tags β€” the 5mC β€” to regulate gene activity. But in 2016, when I was at Yale University, we reported in Nature the discovery that DNA 6mA is also present in mammals,” Wu said. “This finding opened up a whole new set of possibilities in the study of cancer epigenetics.”

Traditional methods of studying 5mC do not capture adenine methylation in mammalian tissues. “This motivated us to develop a new method to profile not only 6mA, but also 4mC and 5mC,” Wu said.

In the current study, published in the journal genome biology, Wu and colleagues report developing a chemical-based sequencing method to quantify several epigenetic markers simultaneously. Their method, called NT-seq, short for nitrite treatment followed by next-generation sequencing, is a sequencing method for detecting multiple types of DNA methylation across the genome. The method can also amplify limited clinical samples, which other methods cannot do.

“We show that NT-seq can detect 6mA, 4mC and 5mC in both bacterial and non-bacterial cells, including mammalian cells,” Wu said. “Compared to other methods, NT-seq is efficient, cost-effective, faster and has a high resolution. Some of its limitations are specific to the specific composition of some genomes. We have suggestions in the article on how to compensate for this limitation.”

“We’re excited about NT-seq,” Wu said. β€œIt can uncover novel DNA methylation patterns or motifs, validate results obtained by other methods, generate data sets for developing machine learning tools for methylation analysis, and pave the way for the epigenetic study of genomic DNA 6mA in non-bacterial organisms, including studies on cancer epigenetics.”

Other contributors to this work include first author Xuwen Li, Shiyuan Guo, Yan Cui, Zijian Zhang, Xinlong Luo, Margarita T. Angelova, Laura F. Landweber, and Yinsheng Wang. The authors are affiliated with one or more of the following institutions: Baylor College of Medicine, University of California Riverside, Columbia University, Baylor’s Huffington Center on Aging, and Dan L Duncan Comprehensive Cancer Center.

This work is supported by grants from CPRIT (RR180072), NIH (R35 ES031707), and a Rivkin Center Scientific Scholar Award.

Source:

Reference magazine:

Li, X., et al. (2022) NT-seq: a chemical-based sequencing method for genomic methylome profiling. Genome Biology. doi.org/10.1186/s13059-022-02689-9†

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