Laboratory of Chromosome Dynamics and Gene Regulation
Principal Investigator
Dr. Gunjan Mehta, Ph.D.
Broad theme 1: Understanding the Dynamic Interactions of SMC Complexes (cohesin and condensin) with Chromatin Throughout the Cell Cycle to Unravel the Mechanism of their Non-Canonical Functions (beyond sister-chromatid cohesion and chromosome condensation, respectively)
Structural Maintenance of Chromosomes (SMC) complexes, cohesin and condensin, are essential molecular machines that organize chromosomes and maintain genome integrity. Beyond their canonical roles in sister chromatid cohesion and chromosome condensation, increasing evidence indicates that these complexes regulate transcription, DNA repair, recombination, and higher-order genome organization. However, the molecular basis of these non-canonical functions remains poorly understood. Our research seeks to determine how the dynamic interactions of SMC complexes with chromatin encode their diverse biological functions throughout the cell cycle. Using state-of-the-art single-molecule imaging and tracking in live Saccharomyces cerevisiae, we directly visualize individual cohesin and condensin subunits and quantify their chromatin-binding dynamics with high spatial and temporal resolution. By measuring chromatin residence times, diffusion coefficients, chromatin-bound fractions, and target-search mechanisms, we investigate how the behavior of individual SMC subunits changes during different stages of the cell cycle. Remarkably, our unpublished studies reveal that the four cohesin subunits exhibit distinct chromatin-binding dynamics, suggesting that individual subunits may contribute differently to cohesin function and regulation. Our recent work (Paliwal et al., 2026) demonstrated that meiotic cohesin exists as two functionally distinct populations: a stable chromatin-bound pool that maintains sister chromatid cohesion and spindle pole body cohesion, and a dynamic pool that promotes loop extrusion, transcriptional regulation, and meiotic recombination. Together with complementary findings in Drosophila and mammalian cells, including evidence for distinct cohesin populations and variable complex stoichiometry, these observations support our central hypothesis that cohesin function is encoded by its dynamic state, molecular composition, and chromatin interaction mode. Furthermore, our recent study demonstrated that meiotic cohesin paralogs exhibit remarkable flexibility in partner choice to govern cell survival, revealing an additional layer of functional plasticity within SMC complexes. By integrating quantitative single-molecule biophysics with chromosome biology, this project aims to uncover fundamental principles of genome organization and identify new molecular mechanisms underlying infertility, cohesinopathies, and cancer.
Figure 2: Schematic overview of the project illustrating how single-molecule imaging and tracking are used to quantify the chromatin-binding dynamics of cohesin and condensin throughout the cell cycle in live Saccharomyces cerevisiae. The study investigates dynamic SMC complex states underlying non-canonical functions in genome organization, transcription, recombination, and chromosome architecture, with implications for infertility, cohesinopathies, and cancer.
Broad theme 2: Quantifying the Dynamic Association of Histone Writers, Readers, and Erasers with Chromatin Using Single-Molecule Tracking in Live Cells in Search of Novel Epigenetic Modulators.
Epigenetic regulation is orchestrated by a diverse network of histone writers, readers, erasers, and ATP-dependent chromatin remodelers that dynamically associate with chromatin to control gene expression, genome stability, and cell fate. While the catalytic activities of these proteins have been extensively characterized, remarkably little is known about how their dynamic interactions with chromatin influence epigenetic regulation in living cells. Our research aims to bridge this knowledge gap by applying state-of-the-art single-molecule tracking microscopy to directly visualize and quantify the chromatin-binding behavior of epigenetic regulators in live budding yeast, fission yeast, and human breast cancer cell lines. We investigate how histone methyltransferases, demethylases, acetyltransferases, deacetylases (including sirtuins), histone readers, and chromatin remodelers search for, recognize, and interact with their chromatin targets. By measuring key biophysical parameters such as chromatin residence time, diffusion coefficients, bound fractions, and target-search mechanisms, we seek to uncover the molecular principles governing epigenetic regulation. We further examine how these dynamics change under diverse genetic, environmental, and pharmacological perturbations, and how they differ between transcriptionally active euchromatin and repressive heterochromatin. An important focus of our work is understanding how the underlying epigenetic landscape influences the recruitment and mobility of chromatin-associated proteins. Beyond providing fundamental insights into chromatin biology, this project explores a new therapeutic paradigm: rather than targeting catalytic domains, we aim to identify strategies that modulate the chromatin-binding dynamics of epigenetic regulators. Such an approach has the potential to selectively reprogram gene expression while minimizing off-target effects, ultimately enabling the development of next-generation epigenetic therapeutics for cancer and other diseases driven by aberrant chromatin regulation.
Figure 3: Schematic overview of the project illustrating how single-molecule tracking is used to quantify the chromatin-binding dynamics of histone writers, readers, erasers, and chromatin remodelers in live yeast and breast cancer cells. The study investigates how chromatin state and perturbations influence protein mobility, residence time, target-search mechanisms, and identifies dynamic chromatin interactions as potential therapeutic targets for epigenetic modulation.
Broad theme 3: Elucidating the functions of chromatin remodelers during meiosis in yeast S. cerevisiae.
Eukaryotic DNA is tightly wrapped around nucleosomes for its compaction to form chromosomes (Fig. 1A). Although this compaction makes it easier to transport DNA (chromosomes) within a dividing cell, it also makes DNA less accessible for the DNA-protein interactions essential for DNA synthesis, repair and transcription. ATP-dependent Chromatin Remodelers (CRs) selectively mobilize nucleosomes leading to nucleosome-depleted chromatin (Fig. 1A) to favor DNA-protein interactions. There are four subfamilies of ATP-dependent CRs in eukaryotes: INO80, CHD/Mi-2, SWI/SNF, ISW1. Several lines of evidence suggest the role of CRs in meiotic recombination. However, the relative contribution of each of the CR complexes and how their absence affects various stages of the meiotic recombination (such as double-strand break (DSB) formation, 5’ end resection, strand invasion and D-loop formation, second end capture and DNA synthesis) is not yet quantified. From the existing literature, it can also be envisioned that CRs may be involved in the other aspects of meiotic chromosome segregation such as cohesin loading, sister chromatid cohesion, centromere function, kinetochore-microtubule attachments, however, it still needs experimental evidence. CRs are also known for regulating the transcription of many genes by making gene promoters accessible for transcription factor binding. Hence, it would be interesting to know how CRs affect the precise timing of the meiotic transcription cascade and possibly delay the meiotic progression in their absence. Recent reports suggest that ~190 meiotic genes have extended transcripts. As CRs are known to regulate promoter accessibility and transcription, it would be interesting to know how CRs maintain the critical balance between the extended and regular transcripts of meiosis-specific genes to regulate the protein levels. We will use a combination of fluorescence microscopy, biochemistry, cell and molecular biology and yeast genetics to explore the functions of CRs in meiosis, a process by which germ cells are produced in humans. As 20% of all human tumors contain mutations in one of the CR complexes, targeting CR pathways is currently evolving as a major therapeutic strategy in the treatment of cancers. Understanding the role of CRs in meiosis has the potential for therapeutic development for treating infertility, stillbirth, genetic disorders and cancers.
Figure 1: A) Multisubunit CR complexes make the chromatin accessible either by evicting or by sliding or by exchanging nucleosomes, B) Spindle dynamics over time during meiosis (immunofluorescence with Tub1 antibodies and DAPI) represents pace of meiotic progression. Scale: 5 µm C) Chromatin spread to quantify the defects in homolog pairing (scale: 2 µm, Ref. 2) and D) synaptonemal complex formation. Scale: 5 µm
Key References:
1) Dey et al. 2026, Scientific Reports (In press)
2) Mehta et al. 2014, Molecular Microbiology 91(6): 1179-1199
3) Hong et al. 2019, Nucleic Acids Research 47(22): 11691-11708
4) Clapier et al. 2017, Nature Reviews Molecular and Cell Biology 18, 407-422