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About Sickkids
About SickKids

David Bazett-Jones, PhD

Research Institute
Director
Advanced Bioimaging Centre

Senior Scientist Emeritus
Genetics & Genome Biology

University of Toronto
Professor
Biochemistry


Phone: 416-813-2181
Fax: 416-813-4931
Email: David.Bazett-Jones@sickkids.ca

Research Interests

PML Nuclear Bodies: PML (promyelocytic leukemia) protein contributes to the formation of typically 5-30 nuclear bodies per cell, depending on the cell type. These bodies range from approximately 0.2 to 1 micron in diameter. Promyelocytic nuclear bodies (PML NBs) are implicated in a number of cellular processes including transcriptional regulation, apoptosis, DNA repair and replication of both viral and cellular DNA. Our laboratory has provided compelling evidence that PML NBs have an intimate connection to chromatin. The striking detail provided by Electron Spectroscopic Imaging (ESI) of PML NBs reveals that 10 nm chromatin fibres  make physical contacts with the protein-based core of the bodies. Our observation of an increase in the number of PML NBs in early S-phase by fission from pre-existing bodies supports a relationship of the bodies with a set of genomic loci. We are now developing new methods to identify the set of cellular genes that associate with PML NBs.

Chromatin structure: Our lab has studied chromatin at a higher structural level through direct visualization of chromatin fibre organization in mammalian nuclei. We have been able to do this with our pioneering development of ESI, which provides quantitative detection and mapping of nitrogen and phosphorus for distinguishing chromatin from protein-based structures and from RNPs.

We have recently confirmed our hypothesis that the global chromatin configuration is critical in pluripotency. This has been supported by imaging studies of: (1) embryonic stem cell differentiation, (2) chromatin structure changes through early mouse embryogenesis and (3) reprogrammed fully differentiated somatic cells into induced pluripotent stem (iPS) cells. The densely-packed chromatin fibres of constitutive heterochromatin domains (chromocentres) in differentiated mouse embryo fibroblasts (MEFs) become highly dispersed in fully reprogrammed iPS cells. The findings of these studies support our hypothesis that a dispersed state of chromatin fibres defines pluripotency.

  • Transcription regulation
  • Nuclear structure and function
  • Development of molecular and cellular imaging techniques

Research Activities

Our hypothesis is that in mammalian cells the activity of a given gene is a function of its three-dimensional location and organization within its chromosome territory and with respect to other "subnuclear organelles" or sub-compartments in the nucleus. Therefore, the transcriptional program of each cell type should correlate with an ultrastructural signature of chromatin domains within the nuclei of cells of a given cell/tissue type.

Promyelocytic leukemia nuclear bodies (PML NBs or NBs) are a class of subnuclear organelles that contribute to the compartmentalization of nuclear proteins. This process must be important because PML NBs play a central role in cellular differentiation and tumour suppression. Indeed, a number of human cancers are characterized by the down regulation or mutations of PML, including acute promyelocytic leukemia, prostate and colon. Though implicated in processes such as transcription, DNA damage repair, and apoptosis, the exact function of PML NBs is not known.

A prevailing model is that they are storage sites of nuclear proteins, serving as platforms from which they move into the nucleoplasm to carry out their functions. By studying the structure, biochemical composition and dynamics of PML NBs, studies from my laboratory support another model. Though our model does not exclude the storage or platform concepts, we propose that PML NBs interact directly with the surrounding chromatin, and thereby perform a more active role in servicing the regulation of genes on their periphery.

Publications

Dellaire G, Bazett-Jones DP. (2007) Beyond repair foci: subnuclear domains and the cellular response to DNA damage. Cell Cycle 6: 1864-1872.

Dellaire G, Ching R, Bazett-Jones DP. (2006) PML nuclear body number increases in early S-phase by a fission mechanism. Journal of Cell Science 119:1026-33.

Dellaire G, Ching RW, Ahmed K, Jalali F, Tse K, Bristow RG, Bazett-Jones DP. (2006) PML nuclear bodies behave as DNA damage sensors whose response to DNA double-strand breaks is regulated by NBS1, and the kinases ATM, Chk2 and ATR. The Journal of Cell Biology, 175: 55-66.

Block GJ, Eskiw CH, Dellaire G, Bazett-Jones DP. (2006) Transcriptional regulation is affected by subnuclear targeting of reporter plasmids to PML nuclear bodies. Molecular and Cellular Biology 26: 8814-8825.

Bazett-Jones, D.P., Li, R., Fussner, E., Nisman, R., Dehghani, H. Elucidating Chromatin and Nuclear Domain Architecture with Electron Spectroscopic Imaging. (2008) Chromosome Research 16: 397-412

Efroni, S., Duttagupta, R.,  Cheng, J., Dehghani, H., Hoeppner, D.J., Dash, C., Bazett-Jones, D.P., Le Grice, S., McKay, R.D.G., Buetow, K.H., Gingeras, T.R., Misteli, T., Meshorer, E. (2008) Global transcriptional activity in pluripotent embryonic stem cells. Cell Stem Cell 2: 437-447.

Torok, D., Ching, R., Bazett-Jones, D.P. (2009) PML nuclear bodies as sites of genetic regulation. (Frontiers in Bioscience 14:1325-1336).

Dellaire, G., Kepkay, R., Bazett-Jones, D.P. (2009) High resolution imaging of changes in the structure and spatial organization of chromatin, gamma-H2A.X and the MRN complex within etoposide-induced DNA repair foci. Cell Cycle  8(22):3750-3769.

Hiratani, I., Ryba, .T., Itoh, M., Rathjen, J., Kulik, M., Papp, B., Fussner, E., Bazett-Jones, D.P., Plath, K., Dalton, S., Rathjen, P.D., Gilbert, D.M.  (2010)  Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Genome Res. 20(2):155-69.

Ahmed, K., Dehghani, H., Rugg-Gunn,P., Fussner, E., Rossant, J, Bazett-Jones, D.P.
(2010) Global chromatin architecture reflects pluripotency and lineage commitment in the early mouse embryo. PLoS One. 5(5):e10531.

Fussner, E., Ching, R., Bazett-Jones, D.P. (2010) Living without the 30 nm chromatin fiber. Trends in Biochem. Sci. 36:1-6.

Fussner, E., Djuric, U., Strauss, M., Hotta, A., Perez-Iratxeta, C., Lanner, F.,  Dilworth, F.J., Ellis, J., Bazett-Jones, D.P. (2011) Constitutive heterochromatin reorganization during somatic cell reprogramming. in press, EMBO J.

A complete list of Dr. Bazett-Jones' publications is available at PubMed