IFOM Nuclear Mechanics & Genome Regulation

Nuclear Mechanics & Genome Regulation

Research Summary

Mechanical signals from the extracellular matrix impinge on cellular geometry resulting in altered functional nuclear landscape and gene expression programs.
These alterations regulate diverse biological processes including stem-cell differentiation, developmental genetic programs and cellular homeostatic control systems. How such signals are integrated to the 3D spatio-temporal organization of the cell nucleus to elicit differential gene expression patterns are poorly understood.
To investigate the biophysical principles underlying these processes, we use a multi-disciplinary approach, combining high resolution imaging of live-cells cultured on micro-patterned substrates, single-cell mechanics and genomics.
Our ongoing work is beginning to provide a quantitative and modular links between cell geometry and nuclear mechanics in regulating 3D chromosome organization and genetic information.
We are now embarking on projects aimed at defining the mechanistic basis for nuclear reprogramming by modulating cell-geometric constraints.
In these projects, we engage in a number of collaborations with both theoretical and experimental groups.

  • Review: Mechanosignaling to cell nucleus and genome regulation G.V.Shivashankar, Annual Reviews of Biophysics, (2011), Vol.40, 361-378
  • Book: Nuclear Mechanics & Genome Regulation (2010) G.V.Shivashankar, Editor, Methods in Cell Biology series, Elsevier Press

 

Theme-1: Structural transitions in nuclear plasticity during stem-cell differentiation

Stem cells are characterized by a highly plastic nucleus with bivalent histone modifications and an active transcriptome. Cellular differentiation programs, induced by physico-chemical signals, result in an increase in cytoplasmic-nuclear ratio, a prestressed nuclear architecture and non-random chromosome organization.
However the mechanisms underlying the structural transitions in nuclear plasticity leading to cell-type specific transcription programs are unclear.
In this project, we mapped the transitions in chromatin compaction states and the emergence of prestressed nuclear organization using mouse embryonic stem-cells cultured on micro-patterned substrates.
Our experiments uncovered an unusual heterogeneity in chromatin assembly and its remodeling. This was also observed during early Drosophila embryogenesis and T-cell differentiation.
These results suggest that such structural transitions in nuclear plasticity are generic and critical modulators of gene expression during differentiation and development.

  • Prestressed Nuclear Organization in Living Cells, Aprotim Mazumder, Roopa T., Abhishek Kumar, K.Venkatesan Iyer, Nisha M Ramdas & G. V.Shivashankar, Methods Cell Biol. (2010) 98, 221-239
  • Emergence of prestressed eukaryotic nucleus during cellular differentiation and development Mazumder A, Shivashankar GV.J R Soc Interface. (2010) Suppl 3:S321-30
  • Integrin adhesion drives the emergent polarisation of active cytoskeletal stresses to pattern cell delamination C Meghana, Nisha Ramdas, Feroz Hameed, Madan Rao, G.V. Shivashankar & Maithreyi Narasimha, Proceedings of the National Academy of Sciences-USA (2011), 108, 9107-9112
  • Mechanical force alters morphogenetic movements and segmental gene expression patterns during Drosophila embryogenesis Abhishek Kumar & G.V. Shivashankar PLoS? One. (2012) 7(3):e33089
  • Developmental heterogeneity in DNA packaging patterns influences T-cell activation and transmigration Soumya Gupta, Shefali Talwar, R.Indulaxmi, Lakshmi R. Perumalsamy, Apurva Sarin & G.V.Shivashankar PLoS? One. (2012) 7(9):e43718
  • Correlated spatio-temporal fluctuations in chromatin compaction states characterize stem cells, Shefali Talwar, Abhishek Kumar, Madan Rao, Gautam Menon and G.V.Shivashankar Biophysical Journal (2013) 104:553-64
  • The C-terminal domain (CTD) in linker histones antagonizes anti-apoptotic proteins to modulate apoptotic outcomes at the mitochondrion. M.Garg, N.Ramdas, M.Vijayalakshmi, G.V.Shivashankar, A.Sarin Cell Death & Disease (2014) 5:e1058
  • The regulation of gene expression during onset of differentiation by nuclear mechanical heterogeneity, Shefali Talwar, Nikhil Jain & G.V.Shivashankar Biomaterials. (2014) 35, 2411-19

 

Theme-2: Coupling between 3D nuclear organization and transcription control

Extracellular matrix signals are integrated to promoter sites, where active recruitment of transcription machinery results in altered gene expression. However the spatio-temporal dynamics underlying such transcription control is unclear.
We show that the 3D organization of chromosome positions was sensitive to global transcription. In addition, within these inter-chromosome territories, the eukaryotic transcription machinery was found to be dynamic.
Further, mechanical activation of cells resulted in chromatin remodeling preceding the nuclear mechanotransduction of transcription co-factors.
Taken together our results suggest that the relative chromosome positions within the 3D architecture of the nucleus may be a major regulator of transcription control; integrating both transcription factors and transcription machinery.

  • Dynamic organization of chromatin assembly & transcription factories in living cells Bidisha Sinha, Dipanjan Bhattacharya, Deepak Kumar Sinha, Shefali Talwar, Shovamayee Maharana, Soumya Gupta & G. V.Shivashankar, Methods Cell Biol. (2010) 98, 57-78
  • Dynamic organization of transcription factories is dependent on functional nuclear architecture Shovamayee Maharana, Divya Sharma, Shi Xianke & G.V. Shivashankar Biophysical Journal (2012) 103:851-859
  • Dynamics of passive and active particles in the cell nucleus Feroz Meeran, Madan Rao & G.V.Shivashankar PLoS? One. (2012) 7(10):e45843.
  • Modeling and experimental methods to probe the link between global transcription and spatial organization of chromosomes K.Venkatesan Iyer, Shovamayee Maharana, Soumya Gupta, Albert Libchaber, Tsvi Tlusty & G.V. Shivashankar PLoS? One. (2012) 7(10):e46628. (Faculty of 1000 publication)
  • Probing Chromatin Structure and Dynamics Using Fluorescence Anisotropy Imaging, Ekta Makhija, K. Venkatesan Iyer, Shefali Talwar & G.V.Shivashankar CRC Handbook, Imaging Biological Mechanics (2014)
  • Super-resolution microscopy reveals decondensed chromatin structure at transcription sites, Yejun Wang, Shovamayee Maharana, Michelle Wang & G.V.Shivashankar Nature Sci Rep. (2014) Mar 26;4:4477

 

Theme-3: Impact of cellular geometry on nuclear mechanics and genome regulation

Cellular differentiation programs in physiology result in distinct cell shapes and nuclear morphology impinging on their function. In addition, depending on cell adhesion, cytoplasmic-nuclear links stabilize prestressed nuclear organization.
This prestressed nuclear organization, determined by cell-geometric constraints, could serve as a substrate to integrate physico-chemical signals to the nucleus to regulate gene expression.
However, the role of distinct cellular geometry in determining the physico-chemical coupling to the nucleus is unclear. Here we used micro-patterned substrates to alter cellular geometry (shape, aspect ratio and size) and study the nuclear homeostatic balance and the mechanotransduction pathways to regulate gene expression.
Perinuclear actin organization was sensitive to cell-geometric constraints leading to actin-flow dependent nuclear rotational dynamics.
In addition, genome-wide transcriptome analysis revealed cell geometry dependent alterations in actin related gene expression.
Importantly, increase in area of cell-substrate interactions reinforced expression of matrix related genes while reduced cell-substrate area resulted in up-regulation of genes involved in cellular homeostasis.
Taken together, our work suggests modularity in switching gene expression patterns by cell geometric constraints.

  • Mechanical activation of cells reveals distinct timescales in chromatin remodelling and MKL nuclear transport Venkatesan Iyer, Stephanie Pulford, Alex Mogilner and G.V.Shivashankar Biophysical Journal (2012) 103:1416-1428
  • Role of actin dependent nuclear deformation in regulating early gene expression, Soumya Gupta, Nimi Marcel, Apurva Sarin and G.V.Shivashankar PLoS?-One. (2012) 7(12):e53031
  • Cell geometric constraints differentially alter cytoplasmic to nuclear signaling to regulate gene expression Nikhil Jain, K.Venkatesan Iyer & G.V.Shivashankar Proceedings of the National Academy of Sciences-USA (2013) 110: 11349-54
  • Model for deformation of cell nucleus by cortical actin layer Gur Fabrikanth, Soumya Gupta, G.V.Shivashankar & Misha Kozlov Biophysical Journal (2013) 105:1316-23
  • Acto-myosin contractility rotates the cell nucleus Abhishek Kumar, Ananyo Maitra, Madhuresh Sumit, Sriram Ramaswamy & G.V. Shivashankar Nature Sci Rep. 2014 Jan 21;4:3781
  • The regulation of dynamic mechanical coupling between actin cytoskeleton and nucleus by matrix geometry Li Qingsen, Abhishek Kumar, Ekta Makhija & G.V.Shivashankar Biomaterials. (2014) 35, 961-69

 

Group members

Phd students
  • Ekta Makhija
  • Nisha Ramdas
  • Yejun Wang

Postdoctoral Fellows
  • Toh Kee Chua
  • Li Qingsen
  • Radhakrishnan
  • Aninda Mitra
  • Prasuna Rao

Research Associates
  • Mallika Nagarjan
  • Shifali Chitrat

Research Assistant
  • Doorgesh Sharma Jokhun

Joint PhD students
  • Aneesh Sathe (with Sheetz lab)
  • Mrinal Shah (with Kenney lab)
  • Xiaowei Shao (with Bershadsky lab)

Past PhD students, year degree awarded & current position
  • Nikhil Jain - (2014) Postdoctoral Fellow, Northwestern University
  • Soumya Gupta - (2013) Medical writer, Singapore
  • Shefali Talwar - (2013) e-Commerce business consultant, India
  • Abhishek Kumar - (2013) Postdoctoral fellow, Yale University, USA
  • Venkatesan Iyer - (2013) Postdoctoral fellow , Max-Plank, Dresden
  • Shovamayee Maharana - (2013) Postdoctoral fellow, Max-Plank , Dresden
  • Feroz Meeran - (2009) Consultant, Bangalore BioCluster?, India
  • Aprotim Mazumder - (2009) Postdoctoral fellow, MIT, USA
  • Dipanjan Bhattacharya - (2008) Postdoctoral fellow, MIT-Singapore, Singapore
  • Bidisha Banerjee - (2007) Assistant Professor, IISER-Kolkata, India
  • Deepak Sinha - (2007) Assistant Professor, IACS-Kolkata, India
  • Gautam Soni - (2006) Assistant Professor, Raman Institute, India
  • T.Roopa - (2006-09) Postdoctoral Fellow, Stanford University

(update: 2014)