Catherine A. Fox

Professor

cfox@wisc.edu

(608) 262-9370

5204C Biochemical Sciences Building
440 Henry Mall, Madison, WI 53706

Catherine Fox

Education

B.S. 1986, University of California-Riverside
Ph.D. 1992, University of Wisconsin-Madison (M. Wickens)
Postdoctoral 1992-96, University of California-Berkeley (J. Rine)

Honors & Awards

Burroughs Wellcome Career Award in Biomedical Sciences, 1996
Shaw Scientist Award, 1998
American Cancer Society Research Scholar, 2002
Vilas Associate Award from the Graduate School, UW-Madison 2005-2007

Research Interests

Our lab wants to understand how different types of chromatin structures have an impact on genome duplication and stability in eukaryotic cells. We use budding yeast (Saccharomyces cerevisiae) as our model organism for many reasons. First, many biochemical and genetic experiments that have defined the mechanisms of genome duplication have been performed in this model organism, providing us with a wealth of knowledge and tools to perform hypothesis-driven experiments in a cellular context. Second, budding yeast are an exceptionally tractable model organism where biochemical, molecular, genetic, microbiological and genomic approaches can be combined to test sophisticated models. Third, because the basic processes we study are well conserved, what we learn in yeast guides the experiments and interpretations from research in more complex eukaryotic organisms. This last point is important because genome duplication and stability are critical for normal cell proliferation and differentiation in multicellular organisms, including humans. Alterations in genome duplication programs, as well as the associated defects in genome stability, are hallmarks of both normal aging and cancerous cells.

Fig1 A ORC is a complex of 6 conserved subunits, Orc1-5 are members of the AAA+ family of ATPases. In yeast, Orc1, Orc4 and Orc5 bind ATP, and Orc1 is responsible for ORC ATPase. B The MCM helicase complex is loaded G1(dhMCM). ORC and Cdc6 bind ATP and DNA to load dhMCM as a head-to-head inert complex of two helicases encircling dsDNA. MCactivators (S-phase M hydrolyzes ATP for this step. C In S-phase, limiting kinases and MCM accessory proteins) activate dhMCM to form 2 CMG helicases that unwind the origin DNA.

DNA replication origins (origins) are a major interest. Origins are the positions on chromosomes where the chromosomal DNA is unwound to allow for new DNA synthesis. Origin winding is the first step of genome duplication and is therefore highly regulated. In eukaryotic cells, this step is tightly coupled to the cell cycle. In G1-phase, multiple proteins and protein complexes, including the Origin Recognition Complex (ORC), work together to load the replicative helicase complex, called the MCM complex. The MCM complex is loaded as an inert double-hexamer containing two hexameric helicases. Only in S-phase is the MCM complex activated and converted into the two active MCM helicases. This activation triggers origin unwinding and the two active helicase holoenzymes, now each encircling single-stranded DNA, will continue to unwind the parental DNA helix for new DNA synthesis. While these basic biochemical steps are now fairly well understood, the field has a comparatively poor understanding of how these steps contend with or are regulated by the complex chromatin structures that that exist in cells. This issue is important because in eukaryotic cells, each chromosome relies on many individual origins physically distributed across its length for its efficient and accurate duplication. Because chromatin structures vary considerably across a chromosome’s length, this fact means that the basic origin machinery must contend with a variety of different chromatin structures. How the core protein-protein and protein-DNA interactions involving the core replication machinery adapt to work in different chromatin environments is unknown.

We are using genetic, genomic and biochemical approaches to define the different chromatin structures that affect the steps required for origin function. We have defined chromatin features that promote the binding of the Origin Recognition Complex (ORC) to DNA, as well as the subsequent loading of the MCM complex in G1. We have also defined chromatin features that can inhibit these steps. We are trying to understand how the various modes of chromatin regulation work with the basic core replication machinery to insure that chromosomes are efficiently and accurately duplicated during cell division.

Publications of Note

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• Hoggard T and CA Fox. 2016. The Origin Recognition Complex in the Initiation of DNA Replication (Chapter 9, pages 159-188) in The Initiation of DNA Replication in Eukaryotic Cells, Editor Daniel L. Kaplan, Springer International Publishing, Switzerland, 2016.

• Hoggard T, Liachko I, Meikle T, Jiang K, Craciun G, Dunham MJ, and CA Fox. 2016. High Throughput Analyses of Budding Yeast ARSs Reveal New DNA Elements Capable of Conferring Centromere-Independent Plasmid Propagation. G3 g3.116.027904. PMC3913637

• Dummer AM, Su Z, Cherney R, Choi K, Denu J, Zhao X and CA Fox. 2016. Binding of the Fkh1 Forkhead Associated domain to a phosphopeptide within the Mph1 DNA helicase regulates mating-type switching in budding yeast. PLoS Genetics, DOI:10.1371/journal.pgen.1006094, 2016. PMC4892509
(Faculty of 1000 Recommended Article)

• Hoggard T, Chang FJ, Perry KR, Subramanian S, Kenworthy J, Chueng J, Shor E, Hyland EM, Boeke JD, Weinreich M and CA Fox. 2018. Yeast heterochromatin regulators Sir2and Sir3 act directly at eukaryotic DNA replication origins. PLoS Genetics May 24;14(5):e1007418. doi: 10.1371/journal.pgen.1007418. PMC5991416.

• Kuznietsov V, Haws S, CA Fox* and JM Denu*. 2018. A universal method for rapid purification of native chromatin fragments. J Biol Chem. Aug 3;293(31):12271-12282. doi: 10.1074/jbc.RA118.002984. Epub 2018 May 24. PMC6078465.