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Modeling regulation of transcription initiation
Descriptive
TitleInfo
Title
Modeling regulation of transcription initiation
Name
(type = personal)
NamePart
(type = family)
Traldi
NamePart
(type = given)
Eliane Zerbetto
NamePart
(type = date)
1975-
DisplayForm
Eliane Traldi
Role
RoleTerm
(authority = RULIB)
author
Name
(type = personal)
NamePart
(type = family)
Mischaikow
NamePart
(type = given)
Konstantin
DisplayForm
Konstantin Mischaikow
Affiliation
Advisory Committee
Role
RoleTerm
(authority = RULIB)
chair
Name
(type = personal)
NamePart
(type = family)
Ebright
NamePart
(type = given)
Richard H
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Richard H Ebright
Affiliation
Advisory Committee
Role
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(authority = RULIB)
internal member
Name
(type = personal)
NamePart
(type = family)
Sengupta
NamePart
(type = given)
Anirvan M
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Anirvan M Sengupta
Affiliation
Advisory Committee
Role
RoleTerm
(authority = RULIB)
internal member
Name
(type = personal)
NamePart
(type = family)
Olson
NamePart
(type = given)
Wilma K
DisplayForm
Wilma K Olson
Affiliation
Advisory Committee
Role
RoleTerm
(authority = RULIB)
internal member
Name
(type = personal)
NamePart
(type = family)
Gedeon
NamePart
(type = given)
Tomas
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Tomas Gedeon
Affiliation
Advisory Committee
Role
RoleTerm
(authority = RULIB)
outside member
Name
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NamePart
Rutgers University
Role
RoleTerm
(authority = RULIB)
degree grantor
Name
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NamePart
Graduate School - New Brunswick
Role
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school
TypeOfResource
Text
Genre
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theses
OriginInfo
DateCreated
(qualifier = exact)
2011
DateOther
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(type = degree)
2011-10
Place
PlaceTerm
(type = code)
xx
Language
LanguageTerm
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(type = code)
eng
Abstract
(type = abstract)
The concept of activation in transcriptional regulation is based on the assumption that product mRNA increases monotonically as a function of regulator concentration. We analyze the Shea-Ackers model of transcription and find this assumption to be correct only for the simplest of promoters. We define a new regulatory constant that is a nonlinear combination of association and transcription initiation constants characterizing activation and repression for more complicated promoters. Our results can guide the synthesis of new promoters and lead to a deeper understanding of the constraints guiding the natural promoters evolution. Using a validated mathematical model based on the Shea-Ackers transcription rate function, we then show that two modes of upregulation have very different effects on the function of promoter PRM in phage lambda. We predict that if CI2 bound to OR2 produced equal increase in RNAP-DNA binding constant (compared to wild-type increase in the closed-open transition probability), the lysogen would be significantly less stable. We then focus on the promoter clearance process during transcription initiation. Our work builds upon an initial sequence-dependent three-pathway model proposed by Xue et al. After making several modifications to this model and not being able to satisfactorily match experimental data, we introduce a new parameter to the model: the possible formation of secondary structure in the single stranded scrunched DNA accumulated before RNA polymerase is able to escape the promoter .
Subject
(authority = RUETD)
Topic
Computational Biology and Molecular Biophysics
RelatedItem
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TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier
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ETD
Identifier
ETD_3567
PhysicalDescription
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electronic resource
InternetMediaType
application/pdf
InternetMediaType
text/xml
Extent
xi, 147 p. : ill.
Note
(type = degree)
Ph.D.
Note
(type = bibliography)
Includes bibliographical references
Note
(type = vita)
Includes vita
Note
(type = statement of responsibility)
by Eliane Zerbetto Traldi
Subject
(authority = ETD-LCSH)
Topic
Genetic transcription—Regulation
Subject
(authority = ETD-LCSH)
Topic
RNA—Synthesis
Identifier
(type = hdl)
http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000063670
RelatedItem
(type = host)
TitleInfo
Title
Graduate School - New Brunswick Electronic Theses and Dissertations
Identifier
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rucore19991600001
Location
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(displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Identifier
(type = doi)
doi:10.7282/T3D50M1F
Genre
(authority = ExL-Esploro)
ETD doctoral
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Rights
RightsDeclaration
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The author owns the copyright to this work.
RightsHolder
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Name
FamilyName
Traldi
GivenName
Eliane
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime
(encoding = w3cdtf);
(qualifier = exact);
(point = start)
2011-09-16 10:02:55
AssociatedEntity
Name
Eliane Traldi
Role
Copyright holder
Affiliation
Rutgers University. Graduate School - New Brunswick
AssociatedObject
Type
License
Name
Author Agreement License
Detail
I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
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Technical
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1382400
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