Guidescan Software For Improved Single And Paired Crispr Guide Rna Design Coupled With Computational Studies In Leukemia
CRISPR technology has revolutionized the field of genome engineering. CRISPR allows for the easy and efficient manipulation of virtually any genetic locus through a two-component system: a CRISPR endonuclease and guide RNA (sgRNA). These components form a complex that enacts double strand breaks in target DNA. The repair of the double strand break is the main mechanism by which genetic editing of a locus takes place. While the endonuclease cleaves target DNA, it is the sgRNA that specifies targets through complementary binding to a target site. Determining the specificity of sgRNAs to their target site represented a crucial challenge to the genome-engineering field. To facilitate the design of CRISPR libraries, we developed Guidescan, a software package that allowed for the customizable production of sgRNA databases that were guaranteed to match user-defined requirements for sgRNA uniqueness. Furthermore, several computational studies of leukemia are described in this thesis that illustrate different molecular actors and mechanisms through which a leukemic like disease, Myelodysplastic Syndrome, can progress towards leukemia, how leukemia hijacks a splicing protein to maintain its pathology, and finally, how a leukemia can develop resistance to a targeted therapy.
CRISPR; GuideScan; Ibrutinib; Musashi2; RBMX
Physiology, Biophysics & Systems Biology
Doctor of Philosophy
Attribution-NonCommercial-NoDerivatives 4.0 International
dissertation or thesis
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