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Zhang, Jingyu (2018) QUANTITATIVE STUDY ON REGULATORY MECHANISMS OF CELL PHENOTYPE TRANSITION. Doctoral Dissertation, University of Pittsburgh. (Unpublished)

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Cells in a multicellular organism share the same set of genome and can assume multiple phenotypes. Uncovering mechanisms of regulating cell phenotype changes has become an important and active research area. This dissertation presents a collection of my combined computational and experimental efforts on studying cell phenotype transitions.
Chapter I gives a literature overview on cell phenotype conversion and regulation. One can identify four generic modules that function coordinately to regulate cell phenotypes. The whole system forms a highly interconnected network and involves a large number of molecular species for epigenetic, transcriptional and translational regulations.
Chapter II addresses how a cell interprets temporal and strength information of signals and makes cell fate decision. I performed an integrated quantitative and computational analysis on how extracellular TGF-β signal is transmitted intracellularly to activate SNAIL1 expression. I demonstrated how quantitative information of TGF-β is distributed through upstream divergent pathways then crosstalk at various places and converge on to SNAIL1. This crosstalk network interprets the duration of TGF-β signal and is robust against stochastic fluctuations.
Chapter III and IV focus on co-regulation of multiple genes that orchestrate cell functions and phenotype changes. In eukaryotic cells, the expression level of a gene is determined by both transcription factors and the local environment, such as histone modifications and three-dimensional chromosome structure. I used EMT in human cell line and neural cell differentiation process in mouse as model systems, respectively. Through performing combined analysis of data of gene expression, epigenetic modification and chromosome conformation, I examined how the local environment and transcriptional factor regulation is coupled. I discovered that genes co-regulated by a common transcription factor (TF) has tendency to be close both sequentially and spatially. The local spatial organization bridged by TFs is cell type specific. Reorganization of DNA local conformation has impact on gene co-regulation during cell phenotype transition.
The final chapter gives a brief summary of the conclusion from my computational and experimental researches in this dissertation. In this chapter, I also introduced the future work in investigating the relationship between chromosome conformation and gene regulation during cell type transition.


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Item Type: University of Pittsburgh ETD
Status: Unpublished
CreatorsEmailPitt UsernameORCID
Zhang, Jingyuzhangjy7@pitt.eduzhangjy70000-0001-6668-2815
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Committee ChairXing, Jianhuaxing1@pitt.eduxing1
Committee MemberBanerjee, Ipsitaipb1@pitt.eduipdb1
Committee MemberLee, Robinrobinlee@pitt.edurobinlee
Committee MemberMa,
Date: 28 August 2018
Date Type: Publication
Defense Date: 6 June 2018
Approval Date: 28 August 2018
Submission Date: 11 August 2018
Access Restriction: 1 year -- Restrict access to University of Pittsburgh for a period of 1 year.
Number of Pages: 161
Institution: University of Pittsburgh
Schools and Programs: School of Medicine > Computational Biology
Degree: PhD - Doctor of Philosophy
Thesis Type: Doctoral Dissertation
Refereed: Yes
Uncontrolled Keywords: Molecular Biology, Bioinformatics
Date Deposited: 28 Aug 2018 18:57
Last Modified: 28 Aug 2019 05:15


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