Department of Biology

Program

Molecular, Cellular & Developmental Biology

Research Areas

• Developmental Mechanisms and Regulation in Eukaryotic Systems
• Eukaryotic Cell Biology, Cytoskeleton and Signaling

Education

Postdoctoral Fellow, Stanford University School of Medicine, 2000-2006
Ph.D., University of Illinois at Urbana-Champaign, 2000
B.S., Honors, University of Wisconsin-Madison, 1994

Awards

2008 Indiana University Trustees Teaching Award
2009-2012 Senior Class Award for Teaching Excellence in Biology
2009 Pew Scholar in the Biomedical Sciences
2010 HHMI/U.S. National Academy of Sciences Summer Institute Fellow
2011 Kavli Fellow of the U.S. National Academy of Sciences

Research Description

Background and Mission
The biochemical circuitry of the cell cycle dictates periods of DNA replication and growth in cells, alternating with the dispersal of genetic and cellular material to their descendents and division. Cells initiate mitosis with synthesis of mitotic cyclins, the activating phosphatase Cdc25 reverses the Wee1-mediated inhibitory phosphorylation of cyclin-dependent kinase 1 (CDK1)/cyclin complexes, and newly activated CDK1 promotes a positive-feedback loop by prompting additional Cdc25 activation (Figure 1). CDK1 then activates an anaphase-promoting complex (APC)-driven negative-feedback loop that targets cyclins for proteolysis, which induces anaphase onset and mitotic exit. Feedback loops such as these are common in signal transduction pathways, but only recently is their functional prominence being studied in terms of the emergent properties that can arise from the “wiring” of a molecular system, like in the stimulus/response relationship between cyclin and CDK1 (Figure 2). The primary driving force behind research in the Pomerening lab is to gain a quantitative understanding of how modules of enzymes are constructed to yield systems that can filter, switch, and oscillate, focusing particularly on M-phase regulation in embryonic and somatic cells, but also in scenarios where these networks have grown corrupt and can no longer properly regulate proliferation. This will be accomplished through quantitative cellular, molecular, and biochemical approaches, but also be underpinned by mathematical approaches in my own laboratory as well as through collaboration with other computational biologists.

Objectives
Currently, the major research objectives of the lab are:

• Dissecting the mechanisms that govern CDK1 activation and discern how the involved signaling players also interface with its APC-driven negative-feedback loop, determine if the M-phase phosphorylation of CDK1 targets is intrinsically linked to its kinetics, and learn the importance of feedback in sculpting the physiological output of a cell from its biochemical inputs during M-phase initiation, progression, and exit;
• Delineating the properties of a somatic cell that adapts its cell cycle regulation from that of the early embryo, determine what similarities and differences exist in the logic of these systems, and identify the roles that positive feedback plays in coupling progression of the cell cycle to CDK1 activity in the embryo and adult;
• Utilizing developed as well as new molecular tools including fluorescent biosensors, inducible expression systems, RNAi, chemical biological, and proteomic approaches to identify kinase targets, study signaling kinetics, and quantitate the effect of signaling pathway perturbations within live cells and cell extracts.

Experimental Systems
For studies of signaling within the context of embryonic stem cells, the Pomerening lab employs the early embryo system of the African clawed frog, Xenopus laevis (see movie here). Xenopus egg cytosol can faithfully reproduce the biochemical context of the cell cycle. In the least, proteins can be depleted, RNA and protein can be added, and stable interphase and mitotic extracts can be produced, as well as cycling egg extracts that reiterate many of the biochemical events that would occur in a cleaving embryo (Figure 3). Multiple consecutive cell cycles can be achieved in this variety of extract (Figure 4) and a bulk of material can be prepared for application in both traditional and more contemporary biochemical methods, and is thus extremely tractable for systems-level studies of the M-phase oscillator and other signaling pathways.

In order to perform quantitative studies of M- phase signaling in somatic cells, we will utilize both transformed (e.g., HeLa) and non-transformed (e.g., fibroblast) cell lines. Several challenges have long existed for dissecting pathways in cells, including the need to chemically synchronize them to  perform biochemical assays, the difficulty in observing and measuring their responses as a result of perturbation, and the inability to perform reverse genetic approaches. By applying live-cell microscopy, fluorescent biosensors, flow cytometry, and RNAi, my laboratory will be empowered to perturb, assess, and effectively wire (or re-wire) the circuits that regulate proliferation and cell-cycle passage in somatic cells (Figure 5).

Select Publications

Ma Y., Yuan X., Wyatt W.R., Pomerening J.R. (2012). "Expression of Constitutively Active CDK1 Stabilizes APC-Cdh1 Substrates and Potentiates Premature Spindle Assembly and Checkpoint Function in G1 Cells." PLoS One:7(3): e33835.

Kang, Q. and Pomerening, J.R. (2012). "Punctuated cyclin synthesis drives early embryonic cell cycle oscillations." Molecular Biology of the Cell: 23: 284-96.

Srividhya, J., Li, Y., and Pomerening J.R. (2011). "Open Cascades as Simple Solutions to Providing Ultrasensitivity and Adaptation in Cellular Signaling." Physical Biology 8(4): 046005.

Pomerening J.R. (2009). "Positive-feedback loops in cell cycle progression." FEBS Letters 2009 Nov 3;583(21):3388-96.

Ferrell J.E. Jr., Pomerening J.R., Kim S.Y., Trunnell N.B., Xiong W., Huang C.Y., Machleder E.M. (2009). "Simple, realistic models of complex biological processes: positive feedback and bistability in a cell fate switch and a cell cycle oscillator." FEBS Letters 83(24):3999-4005.

Pomerening J.R. (2008). "Uncovering mechanisms of bistability in biological systems." Curr Opin Biotechnol. 19(4):381-8.

Tsai T.Y., Choi Y.S., Ma W., Pomerening J.R., Tang C., Ferrell J.E. Jr. (2008). "Robust, tunable biological oscillations from interlinked positive and negative feedback loops." Science 321(5885):126-9.

Pomerening J.R., Ubersax J.A., Ferrell J.E. Jr. (2008). "Rapid Cycling and Precocious Termination of G1 Phase in Cells Expressing CDK1AF." Mol Biol Cell. 19(8):3426-41.

Gong, D., Pomerening, J.R., Myers, J.W., Gustavsson, C., Jones, J.T., Hahn, A.T., Meyer, T., and Ferrell, Jr., J.E. (2007) “Cyclin A2 regulates nuclear-envelope breakdown and the nuclear accumulation of cyclin B1.” Current Biology 17: 85-91.

Hansen, D.V.*, Pomerening, J.R.*, Summers, M.K., Miller, J.J., Ferrell, Jr., J.E., and Jackson, P.K. (2007). “Emi2 at the crossroads: where CSF meets MPF.” (*Co-first authors) Cell Cycle 6: 732-8.

Pomerening, J.R., Kim, S.Y., and Ferrell, Jr., J.E. (2005). “Systems-level Dissection of the Cell Cycle Oscillator: Bypassing Positive Feedback Produces Damped Oscillations.” Cell 122: 565-578.

Pomerening, J.R., Sontag, E.D., and Ferrell, Jr., J.E. (2003). “Building a Cell Cycle Oscillator: Hysteresis and Bistability in the Activation of Cdc2.” Nature Cell Biology 5: 346-51.

Pomerening, J.R., Valente, L., Kinzy, T.G., and Jacobs T.W. (2003). "Mutation of a Conserved CDK Site Converts a Metazoan Elongation Factor 1Bβ Subunit into a Replacement for Yeast eEF1Bα." Molecular Genetics and Genomics 269: 776-88.

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