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Domitilla Del Vecchio. Chen, Pin-Yi. Massachusetts Institute of Technology. Department of Mechanical Engineering. Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science. Massachusetts Institute of Technology. Department of Mechanical Engineering Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science 2020-09-03T17:49:49Z 2020-09-03T17:49:49Z 2020 2020 https://hdl.handle.net/1721.1/127156 1191840983 Thesis: S.M., Massachusetts Institute of Technology, Department of Mechanical Engineering, May, 2020 Thesis: S.M., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, May, 2020 Cataloged from the official PDF of thesis. Includes bibliographical references (pages 77-79). CRISPR-mediated gene regulation is known for its ability to control multiple targets simultaneously due to its modular nature: the same dCas9 effector can target different genes simply by changing the associated gRNA. However, multiplexing requires the sharing of limited amounts of dCas9 protein among multiple gRNAs, leading to resource competition. In turn, competition between gRNAs for the same resource may hamper network function. In this thesis, we develop a general model that takes into account the sharing of limited amounts of dCas9 protein for arbitrary CRISPR-mediated gene repression networks. We demonstrate that, as a result of resource competition, hidden interactions appear, which modifies the intended network regulations. As a case study, we analyze the effects of these hidden interactions on repression cascades. In particular, we illustrate that perfect adaptation to resource fluctuations can be achieved for certain network topology. Then, we analyze the stability properties of uncertain systems that are affected by resource competition via contraction analysis. Finally, we perform a combined analytical and experimental study on a two gRNA parallel network to demonstrate the resource competition effect. by Pin-Yi Chen. S.M. S.M. S.M. Massachusetts Institute of Technology, Department of Mechanical Engineering S.M. Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science 79 pages eng Massachusetts Institute of Technology MIT theses may be protected by copyright. Please reuse MIT thesis content according to the MIT Libraries Permissions Policy, which is available through the URL provided. http://dspace.mit.edu/handle/1721.1/7582 Mechanical Engineering. Electrical Engineering and Computer Science. Resource competition in CRISPR-mediated gene regulation Thesis application/pdf 2020-09-03T17:49:49Z Publication Master MechE EECS unknown unknown <Publication xmlns="https://www.openaire.eu/cerif-profile/1.1/" id="68e1f161-fcaa-4726-8e0d-49402861fa9a"> <Type xmlns="https://www.openaire.eu/cerif-profile/vocab/COAR_Publication_Types">http://purl.org/coar/resource_type/c_1843</Type> <Language>eng</Language> <Title>Resource competition in CRISPR-mediated gene regulation</Title> <PublishedIn> <Publication> </Publication> </PublishedIn> <PublicationDate>2020</PublicationDate> <Authors> <Author> <DisplayName>Chen, Pin-Yi.</DisplayName> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> </Authors> <Editors> </Editors> <Publishers> <Publisher> <DisplayName>Massachusetts Institute of Technology</DisplayName> <OrgUnit /> </Publisher> </Publishers> <License>http://dspace.mit.edu/handle/1721.1/7582</License> <Keyword>Mechanical Engineering.</Keyword> <Keyword>Electrical Engineering and Computer Science.</Keyword> <Abstract>CRISPR-mediated gene regulation is known for its ability to control multiple targets simultaneously due to its modular nature: the same dCas9 effector can target different genes simply by changing the associated gRNA. However, multiplexing requires the sharing of limited amounts of dCas9 protein among multiple gRNAs, leading to resource competition. In turn, competition between gRNAs for the same resource may hamper network function. In this thesis, we develop a general model that takes into account the sharing of limited amounts of dCas9 protein for arbitrary CRISPR-mediated gene repression networks. We demonstrate that, as a result of resource competition, hidden interactions appear, which modifies the intended network regulations. As a case study, we analyze the effects of these hidden interactions on repression cascades. In particular, we illustrate that perfect adaptation to resource fluctuations can be achieved for certain network topology. Then, we analyze the stability properties of uncertain systems that are affected by resource competition via contraction analysis. Finally, we perform a combined analytical and experimental study on a two gRNA parallel network to demonstrate the resource competition effect.</Abstract> <Access xmlns="http://purl.org/coar/access_right" > </Access> </Publication>