University of Dundee

China Scholarship Council: Investigating the role of TET2 in the epitranscriptome of blood cells

The epigenetic mark of DNA methylation is established by DNMT (DNA methyltransferase) enzymes and has been shown to correlate with transcriptional states and influence cell identity and tumorigenesis in mammalian cells. The recent discovery that TET (Ten-Eleven-Translocation) enzymes produce 5-hydromethylcytosine (5hmC), 5-formylcytosine (5fC), 5-carboxycytosine (5caC) and mediate active DNA demethylation in the genome has opened a new avenue to understand how DNA methylation dynamics affect transcriptional programs1Mutations in TET2 and DNMT3A are frequently found (~10-50% of patients) in a wide range of blood diseases, including Acute Myeloid Leukemia (AML) and Myelodysplastic syndrome (MDS). However, the downstream events that cause hematopoietic stem cell to expand and transform following the occurrence of these mutations are currently unknown.   

Genome-wide analysis of DNA methylation patterns has demonstrated that the products of TET-mediated cytosine oxidation (5hmC, 5fC and 5caC) accumulate at gene regulatory elements, especially at promoter-distal enhancer elements. In addition, TET2 binds directly to enhancers and genetic disruption of TET2 in hematopoietic cells results in enhancer DNA hypermethylation. Likewise, deletion of DNMT3A has also been shown to affect enhancer DNA methylation, although with the opposite result (hypomethylation), and to promote cancerous transformation. Thus, the growth advantage observed in TET2- and DNMT3A-mutated cells may be causally related to aberrant DNA methylation at poised and active enhancers that, in turn, leads to deregulation of genes and pathways associated with hematopoietic stem cell differentiation and self-renewal. 

Recent data – from the nascent field of epitranscriptomics - has highlighted the role of TET2 in oxidizing methylcytosine bases to 5hmC in RNA2,3. This PhD project aims to use existing hematopoietic cell lines and cancer models generated in the lab to dissect the role of RNA in the function of TET2 in hematopoiesis. Computational analysis and multi-layered data integration will be performed using novel and established bioinformatics tools. At the completion of this project, the PhD candidate will have obtained a strong skill set in CRISPR-based gene editing, epigenetics and computational biology. 

1Rasmussen KD, Helin K. Role of TET enzymes in DNA methylation, development, and cancer. Genes Dev. 2016 Apr 1;30(7):733-50. doi: 10.1101/gad.276568.115. PMID: 27036965; PMCID: PMC4826392. 

2He C, Bozler J, Janssen KA, Wilusz JE, Garcia BA, Schorn AJ, Bonasio R. TET2 chemically modifies tRNAs and regulates tRNA fragment levels. Nat Struct Mol Biol. 2021 Jan;28(1):62-70. doi: 10.1038/s41594-020-00526-w. Epub 2020 Nov 23. PMID: 33230319; PMCID: PMC7855721. 

3Guallar D, Bi X, Pardavila JA, Huang X, Saenz C, Shi X, Zhou H, Faiola F, Ding J, Haruehanroengra P, Yang F, Li D, Sanchez-Priego C, Saunders A, Pan F, Valdes VJ, Kelley K, Blanco MG, Chen L, Wang H, Sheng J, Xu M, Fidalgo M, Shen X, Wang J. RNA-dependent chromatin targeting of TET2 for endogenous retrovirus control in pluripotent stem cells. Nat Genet. 2018 Mar;50(3):443-451. doi: 10.1038/s41588-018-0060-9. Epub 2018 Feb 26. PMID: 29483655; PMCID: PMC5862756.