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Statistical mechanical modeling of protein-DNA binding

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TitleInfo
Title
Statistical mechanical modeling of protein-DNA binding
Name (type = personal)
NamePart (type = family)
Locke
NamePart (type = given)
George
DisplayForm
George Locke
Role
RoleTerm (authority = RULIB)
author
Name (type = personal)
NamePart (type = family)
Morozov
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Alexandre V
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Alexandre V Morozov
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Advisory Committee
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chair
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Olson
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Wilma K
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Wilma K Olson
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Advisory Committee
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internal member
Name (type = personal)
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Sengupta
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Anivan M
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Anivan M Sengupta
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Advisory Committee
Role
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internal member
Name (type = personal)
NamePart (type = family)
Mekjian
NamePart (type = given)
Aram Z
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Aram Z Mekjian
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Advisory Committee
Role
RoleTerm (authority = RULIB)
internal member
Name (type = personal)
NamePart (type = family)
Case
NamePart (type = given)
David A
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David A Case
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
outside member
Name (type = corporate)
NamePart
Rutgers University
Role
RoleTerm (authority = RULIB)
degree grantor
Name (type = corporate)
NamePart
Graduate School - New Brunswick
Role
RoleTerm (authority = RULIB)
school
TypeOfResource
Text
Genre (authority = marcgt)
theses
OriginInfo
DateCreated (qualifier = exact)
2014
DateOther (qualifier = exact); (type = degree)
2014-10
CopyrightDate (encoding = w3cdtf)
2014
Place
PlaceTerm (type = code)
xx
Language
LanguageTerm (authority = ISO639-2b); (type = code)
eng
Abstract (type = abstract)
Eukaryotes must pack their DNA into the nucleus tightly, yet accessibly. To accomplish this, the nucleus contains special proteins called histones. Histones bind together to form an octamer, and DNA will wrap around the octamer to form a DNA-protein complex called a nucleosome. Nuclesomes are the primary structure of chromatin, which is the assemblage of DNA and proteins that organizes and stores the genome. 75%-90% of the genome is wound into nucleosomes, yet nucleosomes in the wrong place can block the binding of critical proteins including RNA polymerase: nucleosomes must be kept in their proper locations if the cell is to thrive. Therefore, the cell must regulate the positions of its nucleosomes. How does it accomplish this? Experiments that map the locations of nucleosomes reveal that these locations have a variety of sequence signals in common. That is, nucleosomes are more likely to be form from some kinds of DNA sequences than others. This dissertation addresses the sequence specificity of nucleosome formation. We shall seek answers to questions such as the following: What is the causal role of DNA sequence composition in determining nucleosome positions in vivo? If histones prefer some sequences to others, can we predict which sequences are preferable? Can we quantify the degree of preference? How do intrinsic preferences stack up against the many forces operating in the crowded cell nucleus? To address these and related questions, we have investigated genome-wide nucleosome maps produced by the recently established technology known as Next Generation Sequencing – the first such maps became available less than a decade ago. We have developed a flexible model using the formalism of statistical mechanics on a 1-D lattice to model the binding of histones to DNA. Chapter 2 develops this formalism. In Chapter 3, we shall develop a biophysical model of sequence specificity, applying it to maps of nucleosomes in vitro and in vivo from baker’s yeast, otherwise known as S. cerevisiae. Chapter 4 investi- gates the role of in vivo factors in determining chromatin organization in the nematode C. elegans, where our model suggests that effects occurring on the scale of single nucleosomes are responsible for reorganization of chromatin on a length scale several orders of magnitude greater.
Subject (authority = RUETD)
Topic
Physics and Astronomy
RelatedItem (type = host)
TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier (type = RULIB)
ETD
Identifier
ETD_5907
PhysicalDescription
Form (authority = gmd)
electronic resource
InternetMediaType
application/pdf
InternetMediaType
text/xml
Extent
1 online resource (v, 136 p. : ill.)
Note (type = degree)
Ph.D.
Note (type = bibliography)
Includes bibliographical references
Subject (authority = ETD-LCSH)
Topic
DNA-binding proteins
Subject (authority = ETD-LCSH)
Topic
Genomes
Note (type = statement of responsibility)
by George Locke
RelatedItem (type = host)
TitleInfo
Title
Graduate School - New Brunswick Electronic Theses and Dissertations
Identifier (type = local)
rucore19991600001
Location
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NjNbRU
Identifier (type = doi)
doi:10.7282/T37W69WW
Genre (authority = ExL-Esploro)
ETD doctoral
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Rights

RightsDeclaration (ID = rulibRdec0006)
The author owns the copyright to this work.
RightsHolder (type = personal)
Name
FamilyName
Locke
GivenName
George
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime (encoding = w3cdtf); (qualifier = exact); (point = start)
2014-09-25 13:09:37
AssociatedEntity
Name
George Locke
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

RULTechMD (ID = TECHNICAL1)
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ETD
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windows xp
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