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Analysis of targeting mechanisms of tRNA derived fragments (tRFs)

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TitleInfo
Title
Analysis of targeting mechanisms of tRNA derived fragments (tRFs)
Name (type = personal)
NamePart (type = family)
Karaiskos
NamePart (type = given)
Spyros
NamePart (type = date)
1992-
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Spyros Karaiskos
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RoleTerm (authority = RULIB)
author
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Grigoriev
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Andrey
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Andrey Grigoriev
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Advisory Committee
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chair
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Klein
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Eric
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Eric Klein
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Advisory Committee
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internal member
Name (type = personal)
NamePart (type = family)
Nam
NamePart (type = given)
Jongmin
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Jongmin Nam
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Advisory Committee
Role
RoleTerm (authority = RULIB)
internal member
Name (type = personal)
NamePart (type = family)
Ignatova
NamePart (type = given)
Zoya
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Zoya Ignatova
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Advisory Committee
Role
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outside member
Name (type = corporate)
NamePart
Rutgers University
Role
RoleTerm (authority = RULIB)
degree grantor
Name (type = corporate)
NamePart
Camden Graduate School
Role
RoleTerm (authority = RULIB)
school
TypeOfResource
Text
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theses
OriginInfo
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2019
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2019-01
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2019
Place
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xx
Language
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eng
Abstract (type = abstract)
We characterized Drosophila melanogaster tRFs, which appear to have a number of structural and functional features similar to those of miRNAs. These tRFs show a number of similarities with miRNAs, including seed sequences. Based on complementarity with conserved Drosophila regions we identified such seed sequences and their possible targets with matches in the 3’ UTR regions. Strikingly, the potential target genes of the most abundant tRFs show significant Gene Ontology enrichment in development and neuronal function. The latter suggests that involvement of tRFs in the RNA interfering pathway may play a role in brain activity or brain changes with age.
Next, we observed different behavior of two types of tRNA fragments (3’ and 5’ tRFs) detected in significant numbers in rat brains. These fragments showed dynamic changes with age and 3’ tRFs were found to be increasing from young to mid-aged to old rats while 5’ tRFs displayed less consistent patterns. Further, 3’ tRFs showed a narrow range of sizes compared to 5’ tRFs suggesting different biogenesis mechanisms. Putative targets of these fragments were found to be enriched in neuronal and developmental functions.
Last, we describe interactions of human tRFs with their putative target RNAs associated with human Ago1 using Crosslinking, Ligation, And Sequencing of Hybrids (CLASH). We found that Argonaute-loaded tRFs target a wide range of transcripts corresponding to various gene types, in addition to protein-coding transcripts. In the latter, 3' UTR regions are the likely primary target of tRFs, although there is a significant number of interactions of tRFs with coding sequences and a small number of interactions between tRFs and 5' UTR regions. We also report a novel phenomenon – a large number of putative interactions between tRFs and intronic sequences. We analyzed sequences of chimeras formed in vivo between tRFs and their targets to identify clusters of RNA-RNA interaction signatures. We also identified enriched motifs that may be responsible for these interactions and we provide ample evidence supporting the notion that tRF “seed” sequences appear to be primarily located on the 5’ end of a tRF.
Subject (authority = RUETD)
Topic
Computational and Integrative Biology
Subject (authority = ETD-LCSH)
Topic
Transfer RNA
RelatedItem (type = host)
TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier (type = RULIB)
ETD
Identifier
ETD_9379
PhysicalDescription
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electronic resource
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application/pdf
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text/xml
Extent
1 online resource (141 pages : illustrations)
Note (type = degree)
Ph.D.
Note (type = bibliography)
Includes bibliographical references
Note (type = statement of responsibility)
by Spyros Karaiskos
RelatedItem (type = host)
TitleInfo
Title
Camden Graduate School Electronic Theses and Dissertations
Identifier (type = local)
rucore10005600001
Location
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NjNbRU
Identifier (type = doi)
doi:10.7282/t3-59bk-d696
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
Karaiskos
GivenName
Spyros
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime (encoding = w3cdtf); (qualifier = exact); (point = start)
2018-11-30 21:57:41
AssociatedEntity
Name
Spyros Karaiskos
Role
Copyright holder
Affiliation
Rutgers University. Camden Graduate School
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
Type
Embargo
DateTime (encoding = w3cdtf); (qualifier = exact); (point = start)
2019-01-31
DateTime (encoding = w3cdtf); (qualifier = exact); (point = end)
2019-08-02
Detail
Access to this PDF has been restricted at the author's request. It will be publicly available after August 2nd, 2019.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
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