Hinde laboratory: Biophysics of Nuclear Organisation

Researcher

Research Overview

The research focus of the Hinde lab is on the architectural organisation of the cell nucleus and how chromatin dynamics facilitate navigation of the genome.

Inside the nucleus of a living cell, DNA is folded into a multi-layered 3D structure called chromatin. At any moment in time, thousands of proteins are diffusing throughout this structural framework - scanning the genome for a target DNA sequence. The question is “does the chromatin network serve as ‘road map’ for molecular traffic during DNA target search?”

scheme showing the chromatin network of living cells
Figure 1: The chromatin network of living cells.


To investigate this, we are developing microscopy methods - based on fluorescence lifetime and correlation spectroscopy - to track how proteins move throughout the DNA networks of a living cell. Using this technology we have discovered sub-micron rearrangements in chromatin density that direct the diffusive route of DNA repair factors to damage sites and mediate transcription factor accumulation at specific nuclear locations.

Our research to date demonstrates an active role for 3D chromatin organisation in nuclear factor navigation. This is important because a hallmark of cancer is genome dysregulation. We therefore now aim to investigate how disruptions to chromatin structure redirect nuclear traffic and the implications this has for maintaining genome function. The current projects in the lab are:

  1. Mapping the spatial connectivity of nuclear architecture in health and disease
  2. Chromatin dynamics during the DNA damage response
  3. The role of protein oligomerisation in transcription factor DNA target search
scheme showing chromatin dynamics
Figure 2: Chromatin dynamics range from global reorganisation of the genome during the cell cycle on a minute-to-hour timescale (top row) down to nanometer-to-micron rearrangements in local chromatin compaction during the DNA damage response (bottom row).


METHODS

Advanced fluorescence microscopy has revealed molecular insights into the spatial dynamics of biological processes that could not have been obtained by any other means. In the Hinde lab we are applying biophysical methods of analysis based on fluorescence lifetime imaging microscopy (FLIM) and fluorescence fluctuation spectroscopy (FFS) to quantitate protein interaction, aggregation, binding kinetics and diffusion in live cells. For example we use:

  1. Fluorescence lifetime imaging microscopy (FLIM) – FRET biosensor detection
  2. Fluorescence correlation spectroscopy (FCS) – protein diffusion and concentration
  3. Spatiotemporal correlation spectroscopy (STICS, RICS) - protein binding dynamics
  4. Pair correlation analysis (pCF, pCOMB) – spatial route of protein diffusion
  5. Moment based brightness analysis (NB, PCH) – protein oligomerisation

A particular interest of the lab is the development of microscopy methods based on spatial pair correlation function (pCF) analysis to extract the molecular connectivity of nuclear architecture with sub-micron resolution. We have demonstrated that by combining pair correlation analysis with fluorescence lifetime and brightness information we can track nuclear factor complex formation within the structural framework of the nucleus.

Staff

Jieqiong Lou, Post doctoral fellow

Julia Ivanova, Visiting Masters research student

Jee Khor, Honours student

Collaborators

Professor Enrico Gratton, University of California, Irvine, California, USA.
Dr Francesco Cardarelli, National Research Council of Italy, Pisa, Italy.
Dr Anthony Cesare, Children's Medical Research Institute, Sydney, Australia.
Associate Professor Marie Bogoyevitch, University of Melbourne, Melbourne, Australia.
Professor David Jans, Monash University, Melbourne, Australia.
Professor Klaus Hahn, University of North Carolina, Chapel Hill, North Carolina, USA.
Professor Katharina Gaus, University of New South Wales, Sydney, Australia.

Funding

NHMRC Career Development Fellowship (2017-2020) 'Chromatin dyanmics regulate genome function'.
NHMRC Project Grant (2016-2019) 'The role of nuclear architecture in the DNA damage response'.
ARC Discovery Project (2018-2021) 'Nuclear architecture in a living cell facilitates navigation of the genome'.

Research Publications

Click here for the results of a PubMed search of Elizabeth's publications.

Click here for the results of a Google Scholar analysis of Elizabeth's publications.

Hinde E, Pandzic E, Yang Z, Ng IHW, Jans DA, Bogoyevitch MA, Gratton E, Gaus K. Quantifying the dynamics of the oligomeric transcription factor STAT3 by pair correlation of molecular brightness. Nature Communications 2016; 7(11047).

Hinde E, Cardarelli F,  Gratton E. Spatiotemporal Regulation of heterochromatin protein 1 alpha organisation and dynamics in live cells. Scientific Reports 2015; 5:12001: 1-11.

Hinde E,  Kong X,  Yokomori K, Gratton E. Chromatin dynamics during DNA repair revealed by pair correlation analysis of molecular flow. Biophysical Journal 2014; 107(1): 55-65.

Hinde, E,  Digman MA, Hahn KM, Gratton E. Millisecond spatiotemporal dynamics of FRET biosensors by the pair correlation function and the phasor approach to FLIM. PNAS 2013; 110(1): 135-140.

Hinde E,  Cardarelli F, Digman MA, Gratton E. In vivo pair correlation analysis of EGFP intranuclear diffusion reveals DNA-dependent molecular flow. PNAS 2010; 107: 16560-16565.

Research Projects

This Research Group doesn't currently have any projects



Faculty Research Themes

Cancer

School Research Themes

Cancer in Biomedicine, Cell Signalling, Cellular Imaging & Structural Biology, Molecular Mechanisms of Disease



Key Contact

For further information about this research, please contact Head of Research Group Dr Elizabeth Hinde

Department / Centre

Biochemistry and Molecular Biology

Unit / Centre

Hinde laboratory: Biophysics of Nuclear Organisation


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