Studying the nuclear environment through chromatin diffusion

A nucleus expressing two fluorescent proteins. Trf1-RFP stains the telomeres (chromosome ends) in red. H2B-PAGFP is a green fluorescent protein that binds to chromatin and can be activated locally on demand by an external signal. This nucleus will be imaged over a long time range and the motion of the various spots analyzed to reveal the stochastic model controlling their dynamics.

A nucleus expressing two fluorescent proteins. Trf1-RFP stains the telomeres (chromosome ends) in red. H2B-PAGFP is a green fluorescent protein that binds to chromatin and can be activated locally on demand by an external signal. This nucleus will be imaged over a long time range and the motion of the various spots analyzed to reveal the stochastic model controlling their dynamics.

This project aims to understand the organization of chromatin in the cell nucleus. In each cell in our body, approximately two meters of chromatin – the long DNA polymers which hold our genetic information – are maintained in a volume only ten microns across. Past research has shown that these long chains are folded in a hierarchal and ordered fashion, but at the same time exhibit continuous random motions. It is this contradictory folding scenario – systematic organization under constant dynamics – that we try to understand.

Our strategy is based on the understanding that dynamics and structure are deeply connected. They are not two separate phenomena, but rather two sides of the same spatiotemporal framework. Thus by accurately measuring the random motion of various chromatin loci along a broad time range, it is possible to characterize the mechanical causes for these random motions and the stochastic spatial constraints enforced on them. By implementing various biological techniques, we can also characterize the effect of many biochemical interactions, thus gaining better biological and physical understanding of the system.

From the experimental side, our work demands the implementation of an assortment of biological techniques (such as plasmid extraction and transfection) and advanced fluorescent microscopy (including SPT, FRAP, FCS, ICCS and more). The data analysis demands a thorough understanding of random processes, especially various anomalous diffusion models, and the ability to perform large data set characterization. Finally we describe the system through physical models of polymers, viscoelastic media, random energy landscapes and more.

Please feel free to contact us with any question, suggestion or remark.

Related papers:

  1. I. Bronshtein*, E. Kepten* et al. Molecular mechanism for genome organization in the eukaryotic nucleus, Nature Communications, Minor Revisions (2015)    * Equal contribution
  2. E. Kepten, A. Weron, I. Bronshtein, K. Burnecki and Y. Garini, Hubble diffusion description of distance dependent anisotropic chromatin motion. Biophysical Journal, In Review (2015)
  3. K. Burnecki, E. Kepten, Y. Garini, G. Sikora and A. Weron, Estimating the anomalous diffusion exponent for single particle tracking data with measurement errors – An alternative approach. Scientific Reports, Accepted (2015)
  4. E. Kepten, A. Weron, G. Sikora, K. Burnecki and Y. Garini, Guidelines for the fitting of anomalous diffusion mean square displacement graphs from single particle tracking experiments. PLoS ONE 10(2): e0117722 (2015).
  5. E. Kepten, I. Bronshtein and Y. Garini, Improved estimation of anomalous diffusion exponents in single-particle tracking experiments. Physical Review E 87, 052713 (2013).
  6. I. Bronshtein, E. Kepten, and Y. Garini, Single Particle Tracking for Studying the Dynamic Properties of Genomic Regions in Live Cells. Methods in Molecular Biology, Vol. 1042 (2013), Shav-Tal, Yaron (Ed.), Springer
  7. K. Burnecki, E. Kepten, J. Janczura, I. Bronshtein, Y. Garini and A. Weron, Universal Algorithm for Identification of Fractional Brownian Motion. A Case of Telomere Subdiffusion. Biophysical Journal 103(9), 1839-1847 (2012).
  8. E. Kepten, I. Bronshtein and Y. Garini, Ergodicity convergence test suggests telomere motion obeys fractional dynamics. Physical Review E 83, 041919 (2011).
  9. I. Bronstein Berger, Y. Israel, E. Kepten, S. Mai, Y. Shav-Tal, E. Barkai and Y. Garini, Transient anomalous diffusion of telomeres in the nucleus of mammalian cells. Physical Review Letters 103, 018102 (2009).