title: The interplay between chromosome stability and cell cycle control explored through gene-gene interaction and computational simulation.
abstract: Chromosome stability models are usually qualitative models derived from molecular-genetic mechanisms for DNA repair, DNA synthesis, and cell division. While qualitative models are informative, they are also challenging to reformulate as precise quantitative models. In this report we explore how (A) laboratory experiments, (B) quantitative simulation, and (C) seriation algorithms can inform models of chromosome stability. Laboratory experiments were used to identify 19 genes that when over-expressed cause chromosome instability in the yeast Saccharomyces cerevisiae To better understand the molecular mechanisms by which these genes act, we explored their genetic interactions with 18 deletion mutations known to cause chromosome instability. Quantitative simulations based on a mathematical model of the cell cycle were used to predict the consequences of several genetic interactions. These simulations lead us to suspect that the chromosome instability genes cause cell-cycle perturbations. Cell-cycle involvement was confirmed using a seriation algorithm, which was used to analyze the genetic interaction matrix to reveal an underlying cyclical pattern. The seriation algorithm searched over 10(14) possible arrangements of rows and columns to find one optimal arrangement, which correctly reflects events during cell cycle phases. To conclude, we illustrate how the molecular mechanisms behind these cell cycle events are consistent with established molecular interaction maps.
authors.affiliation: School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA 91711, USA Mathematics Department, Claremont Graduate University, Claremont, CA 91711, USA.
authors.forename: Jesse P
authors.initials: JP
authors.lastname: Frumkin
authors.affiliation: School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA 91711, USA.
authors.forename: Biranchi N
authors.initials: BN
authors.lastname: Patra
authors.affiliation: School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA 91711, USA.
authors.forename: Anthony
authors.initials: A
authors.lastname: Sevold
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors.forename: Kumkum
authors.initials: K
authors.lastname: Ganguly
authors.affiliation: School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA 91711, USA.
authors.forename: Chaya
authors.initials: C
authors.lastname: Patel
authors.affiliation: School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA 91711, USA.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Yoon
authors.affiliation: School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA 91711, USA.
authors.forename: Molly B
authors.initials: MB
authors.lastname: Schmid
authors.affiliation: School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA 91711, USA Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA aray@kgi.edu.
authors.forename: Animesh
authors.identifier: 0000-0002-0120-5820
authors.initials: A
authors.lastname: Ray
mesh_terms: D059447:Cell Cycle Checkpoints / Q000235:genetics*; D043171:Chromosomal Instability / Q000235:genetics*; D015825:Chromosomes, Fungal / Q000378:metabolism; D003198:Computer Simulation; D004843:Epistasis, Genetic; D005434:Flow Cytometry; D005800:Genes, Fungal; D008938:Mitosis / Q000235:genetics; D008957:Models, Genetic; D012441:Saccharomyces cerevisiae / Q000166:cytology* / Q000235:genetics*; D013997:Time Factors