Mechanosignaling to Cell Nucleus & Genome Regulation

Cells in culture or within organisms sense mechanical forces on the nanoscale and convert them into physico-chemical signals to regulate genome function. These mechanical signals, as seen in physiology, impinge on cellular differentiation, developmental programs and in eliciting disease phenotypes. How such signals are physico-chemically integrated to the 3D architecture of the cell nucleus to differentially regulate genome function is poorly understood. Our laboratory employs a multidisciplinary approach, using high resolution live-cell imaging combined with single-cell biomechanics and functional genomics, to understand the mechanisms underlying mechanoregulation of genome function. For this we use mouse embryonic stem-cells and T-cells in addition to primary differentiated cells and cell lines as model systems.

Ongoing projects in our laboratory are centered on four themes:

i) Transduction of force via physico-chemical links to the cell nucleus: In this project we are exploring how forces experienced on the plasma membrane of living cells are transmitted to the cell-nucleus. The nucleus is found to be held in a prestressed state: with acto-myosin links providing a tensile force and microtubule networks exerting a compressive load on the nucleus. While a number of chemical signaling events have been shown to be triggered with mechanics, our results also reveal a direct transmission of physical cues to the nucleus - resulting in chromatin remodeling. Ongoing experiments are exploring the various activity dependent molecular intermediates that transduce mechanosignals to the nuclear organization.

ii) 3D genome plasticity & assembly code - spatial control: Recent evidence has revealed a non-random and tissue specific organization of genomes within the cell nucleus. In addition, experiments from other laboratories including ours have shown that the nuclei of stem-cells are found to be highly plastic - transitioning to more rigid structures during cellular differentiation, perhaps establishing cellular transcription memory. Our studies also evidence a spatial assembly code mediating genome organization within the nucleus. In this context, we are now exploring how physical cues that arrive at the nuclear membrane are differentially encoded to gene rich regions to induce spatial control of transcription within the nucleus.

iii) Transcription compartment dynamics - temporal tuning & synchronization:Transcription control in higher organisms is found to be compartmentalized. Genes within the 3D architecture of the cell nucleus have to partner with transcription compartments to elicit function. Using live-cell imaging, we reveal some of the design principles of the dynamic organization of transcription compartments within the cell nucleus. These studies begin to provide an interesting paradigm of integrating cell-mechanics cues to the nucleus by temporal filtering and synchronization of gene position and transcription compartment organization for genome regulation.

iv) Mechanoregulation of gene function -  physiological implications: In physiology, a growing number of examples are being uncovered where mechanical cues induce precise gene expression outputs with functional consequences. We are currently investigating the effect of mechanical cues in two specific model systems; a) induction of early T-cell gene activation markers and b) the expression of morphogenetic patterning genes during Drosophila embryogenesis. These ongoing projects evidence the importance of cell-mechanics cues in regulating gene function in diverse processes as cellular transmigration and morphogenesis.

Selected five publications (2006-2008):

1. Spatio-temporal plasticity in chromatin organization in mouse cell differentiation and during Drosophila embryogenesis Dipanjan Bhattacharya, Shefali Talwar, Aprotim Mazumder & G.V.Shivashankar (Biophysical Journal – in press)

2. Probing the dynamic organization of transcription compartments and gene loci within the nucleus of living cells Deepak Kumar Sinha, Bidisha Banerjee, Shovamayee Maharana, & G.V.Shivashankar Biophysical Journal (2008) 95, 5432-5438

- Accompanied with a new & notable article: Dynamic Organization of Gene Loci and Transcription Compartments in the Cell Nucleus James A. Spudich Biophysical Journal (2008) 95, 5003

3. Dynamics of chromatin decondensation reveals the structural integrity of a mechanically prestressed cell nucleus T.Roopa, Aprotim Mazumder, Aakash Basu, L.Mahadevan & G.V.Shivashankar Biophysical Journal (2008) 95, 3028-3035

4. Gold-nanoparticle-assisted laser ablation of chromatin assembly reveals unusual aspects of nuclear architecture within living cells Aprotim Mazumder & G.V.ShivashankarBiophysical Journal (2007) 93, 2209-2216

5. Chromatin assembly exhibits spatio-temporal heterogeneity within the cell nucleus Bidisha Banerjee, Dipanjan Bhattacharya & G.V.Shivashankar Biophysical Journal (2006), 91, 2297-2303 (Cover page)

While maintaining strong acdemic links with NCBS, TIFR-Bangalore, The Shiva laboratory will soon be moving to the Department of Biological Sciences with affiliations to the Bioengineering Division & the Research Center for Excellence in MechanoBiology at the National University of Singapore. Positions are available for PhD and Postdoctoral fellowships.