Research

Years of concerted efforts by several groups have identified the major key players in DNA repair pathways. But despite this, the connections between DNA damage response (DDR) and the local and global physical structure of the chromatin are only beginning to be discovered. Any corrective responses to DNA damage have to take place in the context of the highly non-random spatial organization within the eukaryotic cell nucleus, which in turn may regulate the processes of transcription and repair in a tissue-specific manner. Indeed there have been suggestions that the tissue-specificity of gene expression is coded at a broad level in the spatial organization of the chromatin. Efforts in my group are focused on elucidating the connections between physical chromatin structure and DDR in tissues with genotoxic stress. Further connecting the themes of tissue-specific gene expression and DDR, we explore the roles of DDR in differentiation and developmental processes, including cancer development. 

It has become increasingly clear that fairly large copy number variations (CNVs) of genetic material can exist among cells in a differentiated tissue. While this is thought to be due to regulated genomic instability, it is not clear if these CNVs serve a functional consequence. It is also known DNA damage pushes undifferentiated embryonic stem cells towards differentiation by repressing pluripotency programs, but again it is not well understood if this differentiation is erratic or lineage-specific. In terms of epigenetic changes too, enzymes evolved for DNA repair can be exploited. In all these contexts, single-cell microscopy experiments in conjunction with current single-cell sequencing efforts could provide unprecedented insight into the regulation of differentiation processes by DNA damage and repair. Over the years, we have developed single-cell level microscopy and image analysis techniques to study the cell cycle dependence of these processes in cells in culture both at the level of transcripts (through single molecule RNA Fluorescence in situ Hybridization) and proteins (through immunofluorescence). Through these studies, we aim to explore if nature generally exploits DDR to regulate processes of differentiation.

In recent years, the mechanical aspects of DDR are being appreciated, and it is an exciting avenue of research, ripe for applications of both physical techniques and rigorous mathematical modeling through collaborative efforts. Our lab aims to develop means to take these experiments to a higher throughput context to gain a systems-level understanding of DDR. 

Presently, the lab is investigating how different HP1 isoforms affect DDR differently; how repair takes place in the context of the special environment of the cell nucleolus; how nuclear mechanics can affect DDR; how temporal control is exerted in the recruitment of factors critical for Nucleotide Excision Repair, and several such directions. 

We have also translated some of our developed techniques to primary tissues both from the fruit-fly and mice. Beyond these fixed cell studies, a  substantial portion of our efforts has gone into live cell studies of the dynamics of DDR and gene expression.