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Molecular systems analysis of a cis-encoded epigenetic switch

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dc.contributor.advisor Gerald R. Fink and Narendra Maheshri. en_US Octavio, Leah M. (Leah Mae Manalo) en_US
dc.contributor.other Massachusetts Institute of Technology. Computational and Systems Biology Program. en_US 2012-01-12T19:27:17Z 2012-01-12T19:27:17Z 2011 en_US 2011 en_US
dc.description Thesis (Ph. D.)--Massachusetts Institute of Technology, Computational and Systems Biology Program, 2011. en_US
dc.description Cataloged from PDF version of thesis. en_US
dc.description Includes bibliographical references. en_US
dc.description.abstract An ability to control the degree of heterogeneity in cellular phenotypes may be important for cell populations to survive uncertain and ever-changing environments or make cell-fate decisions in response to external stimuli. Cells may control the degree of gene expression heterogeneity and ultimately levels of phenotypic heterogeneity by modulating promoter switching dynamics. In this thesis, I investigated various mechanisms by which heterogeneity in the expression of FLO 11 in S. cerevisiae could be generated and controlled. First, we show that two copies of the FLOJ1 locus in S. cerevisiae switch between a silenced and competent promoter state in a random and independent fashion, implying that the molecular event leading to the transition occurs in cis. Through further quantification of the effect of trans regulators on both the slow epigenetic transitions between a silenced and competent promoter state and the fast promoter transitions associated with conventional regulation of FLO11, we found different classes of regulators affect epigenetic, conventional, or both forms of regulation. Distributing kinetic control of epigenetic silencing and conventional gene activation offers cells flexibility in shaping the distribution of gene expression and phenotype within a population. Next, we demonstrate how multiple molecular events occurring at a gene's promoter could lead to an overall slow step in cis. At the FLO] 1 promoter, we show that at least two pathways that recruit histone deacetylases to the promoter and in vivo association between the region -1.2 kb from the ATG start site of the FLO11 ORF and the core promoter region are all required for a stable silenced state. To generate bimodal gene expression, the activator Msnlp forms an alternate looped conformation, where the core promoter associates with the non-coding RNA PWR1's promoter and terminator regions, located at -2.1 kb and -3.0 kb from the ATG start site of the FLO]1 ORF respectively. Formation of the active looped conformation is required for Msnlp's ability to stabilize the competent state without destabilizing the silenced state and generate a bimodal response. Our results support a model where multiple stochastic steps at the promoter are required to transition between the silenced and active states, leading to an overall slow step in cis. Finally, preliminary investigations of heterozygous diploids revealed possible transvection occurring at FLO] 1, where a silenced allele of FLO 11 appeared to transfer silencing factors to a desilenced FLO11 allele on the homologous chromosome. These observations suggest a new mechanism through which heterogeneity in FL011 expression could be further controlled, in addition to the molecular events at the FL011 promoter we elucidated previously. en_US
dc.description.statementofresponsibility by Leah M. Octavio. en_US
dc.format.extent 178 p. en_US
dc.language.iso eng en_US
dc.publisher Massachusetts Institute of Technology en_US
dc.rights M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. en_US
dc.rights.uri en_US
dc.subject Computational and Systems Biology Program. en_US
dc.title Molecular systems analysis of a cis-encoded epigenetic switch en_US
dc.type Thesis en_US Ph.D. en_US
dc.contributor.department Massachusetts Institute of Technology. Computational and Systems Biology Program. en_US
dc.identifier.oclc 768834305 en_US

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