In silico engineering and optimization of Transcription Activator-Like Effectors and their derivatives for improved DNA binding predictions.

Handle URI:
http://hdl.handle.net/10754/583278
Title:
In silico engineering and optimization of Transcription Activator-Like Effectors and their derivatives for improved DNA binding predictions.
Authors:
Piatek, Marek J. ( 0000-0001-5368-3456 )
Abstract:
Transcription Activator-Like Effectors (TALEs) can be used as adaptable DNAbinding modules to create site-specific chimeric nucleases or synthetic transcriptional regulators. The central repeat domain mediates specific DNA binding via hypervariable repeat di-residues (RVDs). This DNA-Binding Domain can be engineered to bind preferentially to any user-selected DNA sequence if engineered appropriately. Therefore, TALEs and their derivatives have become indispensable molecular tools in site-specific manipulation of genes and genomes. This thesis revolves around two problems: in silico design and improved binding site prediction of TALEs. In the first part, a study is shown where TALEs are successfully designed in silico and validated in laboratory to yield the anticipated effects on selected genes. Software is developed to accompany the process of designing and prediction of binding sites. I expanded the functionality of the software to be used as a more generic set of tools for the design, target and offtarget searching. Part two contributes a method and associated toolkit developed to allow users to design in silico optimized synthetic TALEs with user-defined specificities for various experimental purposes. This method is based on a mutual relationship of three consecutive tandem repeats in the DNA-binding domain. This approach revealed positional and compositional bias behind the binding of TALEs to DNA. In conclusion, I developed methods, approaches, and software to enhance the functionality of synthetic TALEs, which should improve understanding of TALEs biology and will further advance genome-engineering applications in various organisms and cell types.
Advisors:
Bajic, Vladimir B. ( 0000-0001-5435-4750 )
Committee Member:
Mahfouz, Magdy M. ( 0000-0002-0616-6365 ) ; Gojobori, Takashi; Gao, Xin ( 0000-0002-7108-3574 ) ; Mijakovic, Ivan
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Program:
Bioscience
Issue Date:
Dec-2015
Type:
Dissertation
Appears in Collections:
Dissertations; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.advisorBajic, Vladimir B.en
dc.contributor.authorPiatek, Marek J.en
dc.date.accessioned2015-12-06T11:42:01Zen
dc.date.available2015-12-06T11:42:01Zen
dc.date.issued2015-12en
dc.identifier.urihttp://hdl.handle.net/10754/583278en
dc.description.abstractTranscription Activator-Like Effectors (TALEs) can be used as adaptable DNAbinding modules to create site-specific chimeric nucleases or synthetic transcriptional regulators. The central repeat domain mediates specific DNA binding via hypervariable repeat di-residues (RVDs). This DNA-Binding Domain can be engineered to bind preferentially to any user-selected DNA sequence if engineered appropriately. Therefore, TALEs and their derivatives have become indispensable molecular tools in site-specific manipulation of genes and genomes. This thesis revolves around two problems: in silico design and improved binding site prediction of TALEs. In the first part, a study is shown where TALEs are successfully designed in silico and validated in laboratory to yield the anticipated effects on selected genes. Software is developed to accompany the process of designing and prediction of binding sites. I expanded the functionality of the software to be used as a more generic set of tools for the design, target and offtarget searching. Part two contributes a method and associated toolkit developed to allow users to design in silico optimized synthetic TALEs with user-defined specificities for various experimental purposes. This method is based on a mutual relationship of three consecutive tandem repeats in the DNA-binding domain. This approach revealed positional and compositional bias behind the binding of TALEs to DNA. In conclusion, I developed methods, approaches, and software to enhance the functionality of synthetic TALEs, which should improve understanding of TALEs biology and will further advance genome-engineering applications in various organisms and cell types.en
dc.language.isoenen
dc.subjectTranscription Activator-Like Effectoren
dc.subjectGenome engineeringen
dc.subjectTALE binding codeen
dc.subjectTALE target predictionen
dc.subjectBioinformaticsen
dc.titleIn silico engineering and optimization of Transcription Activator-Like Effectors and their derivatives for improved DNA binding predictions.en
dc.typeDissertationen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
thesis.degree.grantorKing Abdullah University of Science and Technologyen_GB
dc.contributor.committeememberMahfouz, Magdy M.en
dc.contributor.committeememberGojobori, Takashien
dc.contributor.committeememberGao, Xinen
dc.contributor.committeememberMijakovic, Ivanen
thesis.degree.disciplineBioscienceen
thesis.degree.nameDoctor of Philosophyen
dc.person.id115955en
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