DNA 5-methylcytosine (5mC) as the key epigenetic mark plays crucial roles in cellular biological functions and human diseases such as cancer. It can be oxidised by ten-eleven translocation (TET) family enzymes to 5-hydroxymethylcytosine (5hmC), which can then undergo further oxidation processes and enzymatic removal. Both are abundant and stable epigenetic marks offering significant long-term information, which could be used to classify cell and tissue types. Bisulphite sequencing is regarded as a gold-standard technology to determine the pattern of methylation for decades. However, this method relies on harsh chemical reaction, which degrades the majority of DNA and further limits its applications particularly in low-input samples. In order to overcome the above limitation, a novel bisulphite-free technology, TET-Assisted Pyridine borane Sequencing (TAPS), has been established in our lab. My current research interest is to apply this cutting-edge technology to detect 5mC and 5hmC on third-generation sequencing platforms.
I obtained my Master’s degree in Medicinal and Biological Chemistry from the University of Edinburgh, working on the structural characterisation of cytochrome P450 from Pseudomonas aeruginosa. I then joined the Prof. Tom Brown’s group (Nucleic Acids Research Group) as a DPhil student in the Department of Chemistry at the University of Oxford, where I focused on construction of DNA superstructures functionalised with aptamer moieties for selective cancer cell recognition, intracellular imaging, anticancer drug delivery and sensing specific mRNAs in cancer cells. After obtaining my DPhil degree, I joined Chunxiao Song’s group at Ludwig Institute for Cancer Research as a Post-doctoral researcher in February 2020.
Whole-genome long-read TAPS deciphers DNA methylation patterns at base resolution using PacBio SMRT sequencing technology.
Chen J. et al, (2022), Nucleic acids research, 50
Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution
Liu Y. et al, (2021), Nature Communications, 12
Enzyme-free synthesis of cyclic single-stranded DNA constructs containing a single triazole, amide or phosphoramidate backbone linkage and their use as templates for rolling circle amplification and nanoflower formation
Chen J. et al, (2018), Chemical Science, 9, 8110 - 8120