Our current research includes three themes. First, we are studying the role of non-canonical nucleic acid structures, G-quadruplex (G4) and R-loop in gene expression, both at the level of transcription and translation in e.coli and mammalian cells. G4 is a non-canonical nucleic acid structure that arises from guanine rich sequences of DNA and RNA. There are approximately 400,000 potential G4 forming sequences in the human genome with high enrichment in promoters of oncogenes and regulatory genes and depletion in house-keeping genes and tumor suppressors. Our recent study revealed an unexpected role of G4 in enhancing transcription when formed in the context of transcription mediated R-loop, suggesting a switch-like function of G4 and R-loop (Lee et al, Nature communications, 2021). In parallel, we are examining the role of DNA topology (supercoiling density), G4 helicases (SETX) and RNase H1 which together modulate the G4 and R-loop landscape in genomic DNA.

 

Second, we are investigating a mechanism of telomere maintenance in collaboration with Patricia Opresko lab at University of Pittsburgh. Telomere is a nucleoprotein complex that caps the ends of chromosome for genomic integrity. Six specialized proteins that associate with telomere are termed shelterin. We have elucidated stepwise and directional binding mechanism and dynamic motions imparted by the shelterin proteins when bound to telomeric DNA. More recently, we studied the effect of oxidative lesions (8-oxo-guanine, thymine glycol) on telomere DNA and shelterin association. We are taking on a new direction to study the alternative lengthening of telomere (ALT) pathway that is independent of telomerase mediated mechanism. ALT-positive cancer cells use recombination-based mechanisms to elongate their telomeres. ALT is observed in approximately 10-15% of human cancers, including osteosarcoma, glioblastoma, and pancreatic neuroendocrine tumors. ALT-positive cancers often exhibit unique chromosomal abnormalities, and ALT is associated with a poorer prognosis in some cancer types. The molecular mechanisms underlying ALT are not fully understood, but it is thought to involve the replication of extrachromosomal telomeric DNA circles (T-circles), which serve as templates for the synthesis of new telomeric DNA and a high frequency of telomere sister chromatid exchange (T-SCE). Developing targeted therapies for ALT-positive cancers has been challenging, as the molecular mechanisms underlying ALT are complex and not fully understood. We will focus on elucidating molecular mechanisms responsible for ALT pathway.

 

Third, we are seeking to understanding the molecular underpinning of liquid-liquid phase separation (LLPS). Liquid-liquid phase separation (LLPS) is a cellular process in which molecules with similar properties, such as proteins or nucleic acids, separate from the surrounding environment and form liquid-like droplets within the cell. Recent studies suggest that LLPS may play a role in the pathogenesis of neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobal dementia (FTLD). In ALS, for example, LLPS may lead to the formation of aggregates formed by disordered RNA binding proteins such as FUS and TDP-43, which can undergo LLPS and form liquid-like droplets in the brain and subsequently transition into solid aggregates, which are toxic to neurons and lead to neuronal death. Overall, the role of LLPS in neurodegenerative disease is an active area of research, and further studies are needed to fully understand the mechanisms by which LLPS contributes to disease pathogenesis. We have demonstrated that ALS/FTLD-linked mutations in FUS exhibits prominent molecular defect i.e arginine mutations lead to RNA binding deficiency while glycine mutations result in gelation of FUS condensates. We recently reported a novel mechanism by which poly-(ADP ribose) induce FUS condensation (Mol Cell, 2022).