Aitchison Lab at ISB
Welcome to the Aitchison Lab website

Using yeast cells as research models, the Aitchison lab focuses on applying systems approaches to two fundamental problems in cell biology.

In the first area, of nucleocytoplasmic exchange, the lab studies how proteins selectively gain access to the DNA in the nucleus. Transport factors, termed karyopherins shepherd cargoes through nuclear pores spread over the surface of the cell nucleus. The pores are occupied by large elaborate protein complexes termed nuclear pore complexes. The Aitchison laboratory examines how nuclear pore complexes govern traffic between the nucleus and cytoplasm and how karyopherins, and their respective cargoes selectively transit the pores. As this process is inextricably linked to regulated gene expression, the Aitchison group also studies how this transit system influences the functioning and development of cells.

The Aitchison laboratory also studies peroxisomes: essential cellular organelles that play diverse metabolic roles. Here, the goal is to understand how external signals trigger the development of peroxisomes and how the cell machinery builds and maintains the organelle. The comprehensive understanding of this dynamic process holds promise to provide insight into the biology of peroxisome biogenesis and into the human disease processes linked to peroxisome dysfunction.

In both of these areas, the Aitchison group is applying and developing new technologies in high throughput biology, functional genomics, proteomics, genetics, and computational biology. The group is devoted to merging these systems biology approaches with more traditional cell biological approaches to obtain new fundamental insights into cell biology.

Research Projects:

  • New Tools for Exploring the Dynamic Interactome
  • Center for Systems Biology
  • The Role of Novel Peroxins in Peroxisomal Biogenesis
  • Oleate-responsive gene regulatory networks governing peroxisome proliferation
  • Pilot Project: Isolation and Characterization of RNA Regulatory Machines in Yeast
Affiliations


Adjunct Professor
Department of Cell Biology
Faculty of Medicine, University of Alberta

Adjunct Professor
Department of Biochemistry and Molecular Biology
Faculty of Medicine, University of British Columbia

Affiliate Professor
Department of Biochemistry
University of Washington

Faculty
Molecular and Cellular Biology Program
University of Washington

Key Publications

Smith, J. J., Marelli, M., Christmas, R. H., Vizeacoumar, F. J., Dilworth, D. J., Ideker, T., Galitski, T., Dimitrov, K., Rachubinski, R. A., and Aitchison, J. D. (2002) Transcriptome profiling to identify genes involved in peroxisome assembly and function, J Cell Biol 158, 259-271

Makhnevych, T., Lusk, C. P., Anderson, A. M., Aitchison, J. D., and Wozniak, R. W. (2003) Cell cycle regulated transport controlled by alterations in the nuclear pore complex, Cell 115, 813-823

Marelli, M., Smith, J. J., Jung, S., Yi, E., Nesvizhskii, A. I., Christmas, R. H., Saleem, R. A., Tam, Y. Y., Fagarasanu, A., Goodlett, D. R., Aebersold, R., Rachubinski, R. A., and Aitchison, J. D. (2004) Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane, J Cell Biol 167, 1099-1112

Tackett, A. J., Dilworth, D. J., Davey, M. J., O'Donnell, M., Aitchison, J. D., Rout, M. P., and Chait, B. T. (2005) Proteomic and genomic characterization of chromatin complexes at a boundary, J Cell Biol 169, 35-47

Ramsey, S. A., Smith, J. J., Orrell, D., Marelli, M., Petersen, T. W., de Atauri, P., Bolouri, H., and Aitchison, J. D. (2006) Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast, Nat Genet 38, 1082-1087

Smith, J. J., Ramsey, S. A., Marelli, M., Marzolf, B., Hwang, D., Saleem, R. A., Rachubinski, R. A., and Aitchison, J. D. (2007) Transcriptional responses to fatty acid are coordinated by combinatorial control, Mol Syst Biol 3, 115

Aitchison, J. D., and Wozniak, R. W. (2007) Cell biology: Pore puzzle, Nature 450, 621-622

Saleem, R.A., Knoblach, B., Mast, F.D., Smith, J.J., Boyle, J., Dobson, C.M., Long-O'Donnell, R., Rachubinski, R.A., Aitchison, J.D. (2008) Genome-wide analysis of signalling networks regulating fatty acid induced gene expression and organelle biogenesis, J Cell Biol 2: 281-292

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