Research

The hierarchical model of genome organization is the most accepted model in field. In a hierarchical organization, different levels have dependence on each other and alterations in one level should get transmitted to other levels lying below or above it, resulting in "Bottom-Up" and "Top-Down" causation properties. We are testing the strength of the hierarchical nature of 3D chromatin orgnization by perturbing a particular level and monitor its effects on other levels of organization. Our data show that disruption of self-association of a polycomb protein, polyhomeotic, PH (PH-PH interaction) disrupts chromatin contacts, decreases nucleosome occupancy and alter accessibility. Polymer simulations investigating the interplay between distant chromatin contacts and nucleosome occupancy, both of which are regulated by PH polymerization, suggest that nucleosome density increases when contacts between different regions of chromatin are established. These results suggest that higher-order organization (chromatin contacts) modulate lower level of organization, nucleosomes -"Top-Down" causation. (Amin et al., Life-Science Alliance, 2023).

In another study we investigated the relationship between nucleosome-level organisation and higher-order chromatin organization by perturbing nucleosomes across the genome by deleting Imitation-SWitch(ISWI) and Chromodomain Helicase DNA-binding(CHD1) chromatin remodeling factors in budding yeast .We find the changes  in nucleosome-level properties are accompanied by changes in 3D chromatin organisation. Change in nucleosome positioning seems to alter the stiffness of chromatin, which can affect formation of chromatin contacts. Our results suggest a biomechanical ‘’bottom-up’’ mechanism by which nucleosome distribution across genome shapes 3D chromatin organisation (Fouziya et al., Science Adv. 2024).

ATP-dependent chromatin remodeling probed by hydrogen/deuterium exchange-mass spectrometry

Chromatin remodelers maintain chromatin structure and hence, gene expression. Imitation Switch, ISWI is achromatin remodeler which regulates nucleosome spacing across the genome by its adenosine 5’-triphosphate (ATP)-dependent nucleosome sliding activity. To understand how this happens requires the identification of the conformational changes that occur in all domains of ISWI during the entire nucleosome sliding cycle. Using the hydrogen-deuterium-exchange coupled to Mass-Spectrometry (HDX-MS) methodology, we have monitored the conformational dynamics of Drosophila FL-ISWI at all the stages ofnucleosome sliding. Our data show that in the resting-state, FL-ISWI is intrinsically dynamic in many regions including the N- and C-terminal regulatory regions (shown above). During nucleosome sliding, different regions of the ATPase-domain, which bind to the nucleosomal DNA, undergo major conformational change, and the C-terminal HSS domain switches from a stable state to a more dynamic state. ISWI adopts distinctconformations in its nucleosome-bound and sliding-states, as the interactions established by it upon binding to the nucleosome are broken during DNA translocation. HDX-MS has made it possible to characterizemulti-scale dynamics from small fluctuations to large structural changes occurring in all the domains of FL-ISWI during the different steps of nucleosome sliding. The structural mechanism revealed for ISWI has implications for several other protein families containing a Rec-A domain ATPase core. (Bhat et al., Biochemistry, 2025)

3D Genome Pathologies

Only about 2% of human genome codes for proteins/RNAs and function of  98% of the genome remains to be found, therefore earning the name of "Dark Genome". Although, it is relatively easy to understand the implications of mutations in coding  part of the genome, it has turned out very challenging to understand the implications of mutations in non-coding genome. Many regulatory sequences are belived to form a part of the non-coding genome. We are interested in investigating the role of non-coding dark genome in regualting organization and function of genome. We are presently focusing on identifying sequence variations/mutations in non-coding genome related to GI cancers and rare diseases. We apply epidemiology, Whole Genome Sequencing and DL/ML based computaional methods to address this problem.