Cell cycle control is highly conserved through the eukaryotic kingdom, and the budding yeast model system has been the source of major insights applicable to issues in human development and disease. This proposal continues systems-level analysis of the eukaryotic cell cycle using this model system. The cell cycle 'clock'functions with high reliability and low noise, even though individual components and circuits making up the clock are frequently known to be highly variable. For example, gene expression is known to be highly variable between individual cells, and yet cell-cycle-regulated gene expression can be highly reliable with respect to timing and amplitude. Threshold responses to rising cyclin-Cdk activity levels can provide switch-like behavior, but such switches can frequently come at the cost of highly variable onset time; the overall cell cycle control circuitry avoids this variability. We are pursuing an emerging concept of multiple independent oscillators contributing to cell cycle control;while uncoupled oscillators result in highly variable and irregular sequences of cell cycle events, we propose that coupling ('phase-locking') of otherwise independent oscillators to the central cyclin-Cdk oscillator can yield a robust and accurate overall system. This proposal continues our innovative use of quantitative time-lapse fluorescence microscopy, over multi-cell cycle timescales, combined with semi-automated image analysis and in-depth genetic and quantitative analysis to drive systems-level understanding of cell cycle control. We are developing new methods of mathematical modeling. There is a pressing need in biology for simple but experimentally constrained models that can reveal basic control principles. The challenge is to find the most illuminating balance between the detail required for a connection to biological reality, and model simplicity required for transparency and insight. We are exploring methods to use geometrical, low-dimensionality representations of the cell cycle control network that can still be experimentally constrained, and that will yield testable predictions. In a new direction to provide evolutionary contrast from a critical but underexplored branch of the eukaryotic kingdom, we will carry out a genetic screen aiming at saturated detection of cell cycle control elements in the green alga, Chlamydomonas reinhardtii. We have devised robotic methods for the microbiology of mutant isolation, which combined with deep sequencing, allows a massive speedup of this project compared to traditional means.

Public Health Relevance

Cell division is a central process in growth and development of all organisms, which must be tightly regulated to provide new cells only at the right time and place. While we understand a lot about individual sub-mechanisms of cell cycle control, we do not understand how these potentially noise-ridden components work together to yield reliable control. We study this question in the experimentally tractable budding yeast. For broader evolutionary perspective, we have also initiated a search for cell cycle control elements in green algae. Green algae diverged from animal and yeast lineages long before they diverged from each other, so learning about all three provides triangulation on basic eukaryotic principles;at the same time, paradoxically, green algae have greater conservation of some critical animal cell cycle control proteins than do yeast. Thus green algae provide the sole system for microbial genetic exploration of functions of the proteins, such as the retinoblastoma protein and cyclin A.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM078153-05
Application #
8237988
Study Section
Cellular Signaling and Regulatory Systems Study Section (CSRS)
Program Officer
Hamlet, Michelle R
Project Start
2006-08-01
Project End
2015-12-31
Budget Start
2012-01-01
Budget End
2012-12-31
Support Year
5
Fiscal Year
2012
Total Cost
$339,000
Indirect Cost
$139,000
Name
Rockefeller University
Department
Genetics
Type
Other Domestic Higher Education
DUNS #
071037113
City
New York
State
NY
Country
United States
Zip Code
10065
Li, Yinyin; Cross, Frederick R; Chait, Brian T (2014) Method for identifying phosphorylated substrates of specific cyclin/cyclin-dependent kinase complexes. Proc Natl Acad Sci U S A 111:11323-8
Tulin, Frej; Cross, Frederick R (2014) A microbial avenue to cell cycle control in the plant superkingdom. Plant Cell 26:4019-38
Zhang, Qian; Yoon, Youngdae; Yu, Yaxin et al. (2013) Stochastic expression and epigenetic memory at the yeast HO promoter. Proc Natl Acad Sci U S A 110:14012-7
Bai, Lu; Ondracka, Andrej; Cross, Frederick R (2011) Multiple sequence-specific factors generate the nucleosome-depleted region on CLN2 promoter. Mol Cell 42:465-76
Cross, Frederick R; Buchler, Nicolas E; Skotheim, Jan M (2011) Evolution of networks and sequences in eukaryotic cell cycle control. Philos Trans R Soc Lond B Biol Sci 366:3532-44
Bai, Lu; Charvin, Gilles; Siggia, Eric D et al. (2010) Nucleosome-depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle. Dev Cell 18:544-55
Charvin, Gilles; Oikonomou, Catherine; Siggia, Eric D et al. (2010) Origin of irreversibility of cell cycle start in budding yeast. PLoS Biol 8:e1000284
Oikonomou, Catherine; Cross, Frederick R (2010) Frequency control of cell cycle oscillators. Curr Opin Genet Dev 20:605-12
Lu, Ying; Cross, Frederick R (2010) Periodic cyclin-Cdk activity entrains an autonomous Cdc14 release oscillator. Cell 141:268-79
Di Talia, Stefano; Wang, Hongyin; Skotheim, Jan M et al. (2009) Daughter-specific transcription factors regulate cell size control in budding yeast. PLoS Biol 7:e1000221

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