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Function analysis of the Arabidopsis epigenome through integrating genome-wide profiles and cell-type-specific approaches
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TitleInfo
Title
Function analysis of the Arabidopsis epigenome through integrating genome-wide profiles and cell-type-specific approaches
Name
(type = personal)
NamePart
(type = family)
Luo
NamePart
(type = given)
Chongyuan
NamePart
(type = date)
1986-
DisplayForm
Chongyuan Luo
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(authority = RULIB)
author
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Lam
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(type = given)
Eric
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Eric Lam
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Advisory Committee
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chair
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Dooner
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Hugo K
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Hugo K Dooner
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Advisory Committee
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internal member
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Jelenkovic
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Gojko
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Gojko Jelenkovic
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Advisory Committee
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internal member
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Gartenberg
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Marc
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Marc Gartenberg
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Advisory Committee
Role
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(authority = RULIB)
outside member
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NamePart
Rutgers University
Role
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(authority = RULIB)
degree grantor
Name
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Graduate School - New Brunswick
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school
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Text
Genre
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theses
OriginInfo
DateCreated
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2012
DateOther
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(type = degree)
2012-05
Place
PlaceTerm
(type = code)
xx
Language
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(type = code)
eng
Subject
(authority = RUETD)
Topic
Plant Biology
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TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier
(type = RULIB)
ETD
Identifier
ETD_3916
PhysicalDescription
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electronic resource
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Extent
xviii, 200 p. : ill.
Note
(type = degree)
Ph.D.
Note
(type = bibliography)
Includes bibliographical references
Note
(type = statement of responsibility)
by Chongyuan Luo
Abstract
(type = abstract)
The eukaryotic epigenome is a dynamic ensemble of chromatin modifications and
chromatin structure variations. Its complexity demands experimental methods for the
global profiling of epigenomic features as well as informatics tools that facilitate data
analyses. I developed Chromatin Immunoprecipitation coupled with high-throughputsequencing (ChIP-seq) to interrogate histone modifications in the model plant Arabidopsis thaliana. Using the ChIP-seq and RNA-seq methods, I produced profiles of nine histone modifications and the transcriptome from aerial tissues of mature plants. With ANchored CORrelative Pattern (ANCORP) method, our analysis has delineated 42 chromatin states with distinct chromatin modification patterns. Selected states were tested by re-ChIP assay to validate the co-localization of histone modifications. I identified the enrichment of Gene Ontology, microRNAs and transposable elements in certain chromatin states, which suggests the regulation of these loci with chromatin-related mechanisms. To derive hypotheses regarding the interactions between the epigenome and transcriptome, State-Specific-Effects-Analysis (SSEA) was developed to incorporate quantitative information related to chromatin states to improve the sensitivity of correlative analyses. Combining ANCORP and SSEA, I identified correlations between
the quantity of Natural Antisense Transcripts (NATs) and the enrichment of H3K36me2
and 5mC marks. Genetic analyses identified Polymerase Associated Factors as potential
regulators for NAT abundance. I further observed evidence for both nuclear- and
cytoplasmically-localized NATs. Although some nuclear-localized NATs are known to
regulate chromatin-related functions, our results suggest that NATs may not commonly
regulate the cognate locus in cis. Differentiation of distinct cell types is fundamental to the sophisticated body-plan and lifestyle of multicellular organisms. Therefore studying the epigenome in specific cell types is critical for elucidating the function of epigenetic regulation in plant development. I experimented with two different cell/nucleus isolation techniques –Fluorescence Activated Cell Sorting (FACS) and Isolation of Nuclei TAgged in specific Cell Types (INTACT) for performing epigenomic profiling in specific plant cell types. I showed that Arabidopsis root cells labeled with GFP can be effectively isolated with
FACS. I initiated the effort to establish a high-throughput and Gateway-compatible
INTACT platform for investigating interactions between key regulators and chromatin
modifications in root cell layers. Our strategy and progress in this front will be described
chromatin structure variations. Its complexity demands experimental methods for the
global profiling of epigenomic features as well as informatics tools that facilitate data
analyses. I developed Chromatin Immunoprecipitation coupled with high-throughputsequencing (ChIP-seq) to interrogate histone modifications in the model plant Arabidopsis thaliana. Using the ChIP-seq and RNA-seq methods, I produced profiles of nine histone modifications and the transcriptome from aerial tissues of mature plants. With ANchored CORrelative Pattern (ANCORP) method, our analysis has delineated 42 chromatin states with distinct chromatin modification patterns. Selected states were tested by re-ChIP assay to validate the co-localization of histone modifications. I identified the enrichment of Gene Ontology, microRNAs and transposable elements in certain chromatin states, which suggests the regulation of these loci with chromatin-related mechanisms. To derive hypotheses regarding the interactions between the epigenome and transcriptome, State-Specific-Effects-Analysis (SSEA) was developed to incorporate quantitative information related to chromatin states to improve the sensitivity of correlative analyses. Combining ANCORP and SSEA, I identified correlations between
the quantity of Natural Antisense Transcripts (NATs) and the enrichment of H3K36me2
and 5mC marks. Genetic analyses identified Polymerase Associated Factors as potential
regulators for NAT abundance. I further observed evidence for both nuclear- and
cytoplasmically-localized NATs. Although some nuclear-localized NATs are known to
regulate chromatin-related functions, our results suggest that NATs may not commonly
regulate the cognate locus in cis. Differentiation of distinct cell types is fundamental to the sophisticated body-plan and lifestyle of multicellular organisms. Therefore studying the epigenome in specific cell types is critical for elucidating the function of epigenetic regulation in plant development. I experimented with two different cell/nucleus isolation techniques –Fluorescence Activated Cell Sorting (FACS) and Isolation of Nuclei TAgged in specific Cell Types (INTACT) for performing epigenomic profiling in specific plant cell types. I showed that Arabidopsis root cells labeled with GFP can be effectively isolated with
FACS. I initiated the effort to establish a high-throughput and Gateway-compatible
INTACT platform for investigating interactions between key regulators and chromatin
modifications in root cell layers. Our strategy and progress in this front will be described
Subject
(authority = ETD-LCSH)
Topic
Arabidopsis
Subject
(authority = ETD-LCSH)
Topic
Eukaryotic cells
Subject
(authority = ETD-LCSH)
Topic
Chromatin
Identifier
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http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000065199
RelatedItem
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TitleInfo
Title
Graduate School - New Brunswick Electronic Theses and Dissertations
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rucore19991600001
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NjNbRU
Identifier
(type = doi)
doi:10.7282/T38W3C7C
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
(type = personal)
Name
FamilyName
Luo
GivenName
Chongyuan
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime
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(qualifier = exact);
(point = start)
2012-04-12 00:56:33
AssociatedEntity
Name
Chongyuan Luo
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.
RightsEvent
DateTime
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(qualifier = exact);
(point = start)
2012-05-31
DateTime
(encoding = w3cdtf);
(qualifier = exact);
(point = end)
2014-05-31
Type
Embargo
Detail
Access to this PDF has been restricted at the author's request. It will be publicly available after May 31st, 2014.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
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Statistical Profile