Ten-Eleven-Translocation (TET) proteins are dioxygenases that oxidize 5-methylcytosine to 5-hydroxymethyl- (5hmC), 5-formyl- (5fC) and 5-carboxyl- (5caC) cytosine (together known as oxidized-methylcytosines or oxi-mCs) to mediate DNA demethylation. Our initial studies showed that TET activity mediates recruitment of transcription factors essential for activation of specific enhancer elements during B cell differentiation (Science Immunology, 2019). The activity of TET enzymes is also known to be diminished in many solid cancers and hematological malignancies, including B-cell lymphomas. However, the molecular mechanisms by which TET enzymes suppress oncogenesis are not fully understood. Our recent studies showed increased accumulation of G-quadruplexes and R-loops upon TET deficiency in B cells and other hematopoietic cells. This is intriguing because G-quadruplexes and R-loops have been linked to genomic instability in various cellular systems, which is also a known feature of TET deficiency. Together, these studies suggest a molecular mechanism by which TET loss-of-function predisposes to genomic instability and cancer. In light of these findings, we are now actively interested in devising therapeutic strategies for targeting cancers with TET loss-of-function.
We are currently investigating mechanisms by which TET activity might regulate the dynamics of G-quadruplex and R-loop structures. G-quadruplexes and R-loops are dynamic structures that are regulated by the recruitment of transcription machinery and the concerted action of helicases and nucleases that resolve them. The catalytic activity of TET enzymes is also known to be transcriptionally linked, and we aim to test how TET activity controls the homeostatic regulation of G-quadruplexes and R-loops. This work will not just reveal mechanisms regulating the dynamics and localization of G-quadruplex and R-loop structures but will also have a major impact on our understanding of basic transcriptional control.
G-quadruplexes were first described several decades ago, but their existence in the mammalian genome was conclusively proven only recently. Using specific methods for identification and predictive computational tools, studies have revealed associations of G-quadruplexes with key regulatory regions in the mammalian genome. G-quadruplex DNA sequences are found at almost 40% of all human gene promoters (particularly, at oncogenes), 90% of DNA replication origins, CpG islands, 5’UTRs of ~3000 genes, active transposable elements and telomeric repeats in several organisms. However, the biological significance of G-quadruplexes at these sites and the molecular pathways they regulate remain ambiguous. Towards this, our recent work has identified many key nuclear protein complexes as novel G-quadruplex binders. These protein complexes are important for regulating diverse aspects of genome biology, such as, nucleosomal remodeling, histone modifications, transcription initiation/elongation and genomic compartmentalization. We are following up on these leads to study G-quadruplexes as key determinants of genome structure and function.
