Adam Rudner
Assistant Professor

Degrees:

B.S. Yale University, 1992
Ph.D. UC, San Francisco, 2000
Post-doctoral Research at UC, San Francisco and Harvard Medical School

Big Questions:

How do cells assemble chromosomal structures and regulate chromosome dynamics?

How do cell physiology, environmental conditions and developmental cues regulate these processes?

Research Interests:

Work in my lab is focused on understanding fundamental problems of chromosome dynamics. Defects in chromosome structure and segregation can lead to chromosome loss and damage, both critical events in the development of cancer and chromosomal disorders. We use the budding yeast, Saccharomyces cerevisiae, as a model for understanding the assembly and regulation of chromosomes. Budding yeast is a terrific model because most cell biology is well conserved between yeast and larger cells and yeast provides a facile genetic and biochemical system in which hypotheses can be rapidly and rigorously be tested. Budding yeast is also amenable to proteomic techniques, and the projects in the laboratory make use of the ease of purifying protein complexes in yeast, and then identifying all their components, as well as their post-translational modifications.

Purification of Heterochromatin

Like heterochromatin in other organisms, heterochromatin (or silent chromatin) in yeast is a repressive chromatin structure that is late replicating, refractory to transcription and recombination, and is epigenetically inherited. Silent chromatin in budding yeast assembles from a complex of Sir2, Sir3 and Sir4 (the SIR complex) and spreads along hypoacetylated regions of chromatin. Genetic screens have identified other proteins that are involved in initiating the assembly of silent chromatin, but no method has allowed a systematic identification of the complete set of proteins physically present in this repressive chromatin domain.

In order to determine the precise structure and protein composition of silent chromatin we have developed a method of biochemically purifying fragments of native silent chromatin. As expected, these fragments contain the SIR complex, histones, as well as proteins that initiate silent chromatin assembly. In addition we find known chromatin proteins as well as other proteins with unknown roles in chromosome metabolism.

Our lab is currently characterizing a number of novel silencing complexes, and using proteomic techniques to discover how the composition and stochiometry of these complexes change in response to changing cell physiology. This methodology will also be used to expand our studies to additional chromosomal loci.

The Phosphoproteome of the Anaphase Promoting Complex

The exit from mitosis in eukaryotes is triggered by the regulated destruction of anaphase regulators by the Anaphase Promoting Complex (APC), a multi-subunit ubiquitin ligase. In yeast, the APC is composed of thirteen subunits and its activity is regulated by the binding of activating subunits, the presentation of its substrates, and by its phosphorylation. The cyclin dependent kinase, Cdk1, phosphorylates the APC and this phosphorylation is required for its activation during mitosis. In an effort to determine if phosphorylation regulates other aspects of APC function we are determining the complete phosphoproteome of the APC using mass spectrometry. To date we have identified many new phosphorylation sites on eight of the thirteen subunits. We are now using stable isotope labeling by amino acids in cell culture (SILAC) and absolute quantification (AQUA) to identify which sites are regulated during the cell cycle and in response to changes in cell physiology, as well to determine which kinases and phosphatases regulate APC phosphorylation.

Selected Publications:

Li, X., Gerber, S.A., Rudner, A.D., Beausoleil, S.A., Haas, W., Villen, J., Elias, J.E., Gygi, S.P. Large-Scale Phosphorylation Analysis of -Factor-Arrested Saccharomyces cerevisiae. 2007. Journal of Proteome Research. Full paper

Rudner, A.D., Hall, B.E., Ellenberger, T., Moazed, D. A non-histone protein-protein interaction required for the assembly of the SIR complex and silent chromatin. 2005. Molecular and Cellular Biology. 25, 4514-4528. Full Paper

Denison C., Rudner A.D., Gerber S.A., Bakalarski C.E., Moazed D., Gygi S.P. 2005. A Proteomic Strategy for Gaining Insights into Protein Sumoylation in Yeast. Molecular and Cellular Proteomics. 2005. 4, 246-254 Nov 12. Full Paper

Moazed D., Rudner A.D., Huang J., Hoppe G.J., Tanny J.C. A model for step-wise assembly of heterochromatin in yeast. 2004. Novartis Foundation Symposium. 259, 48-56.

Hoppe, G.H., Tanny, J.C., Rudner, A.D., Gerber, S.A., Danaie, S., Gygi, S., Moazed, D. 2002. Steps in assembly of silent chromatin in yeast: Sir3-independent binding of a Sir2/Sir4 complex to silencers and role for Sir2-dependent deacetylation. Molecular Cellular Biology. 22, 4167-4180. Full Paper

Rudner, A.D., Hardwick, K.G. and Murray, A.W. 2000. Cdc28 activates the exit from mitosis. Journal of Cell Biology. 149, 1361-1376. Full Paper

Rudner, A.D., and Murray, A.W. 2000. Phosphorylation by Cdc28 activates the Cdc20-dependent activity of the anaphase promoting complex. Journal of Cell Biology. 149, 1377-1390. Full Paper