diplomsko delo
Gregor Spruk (Author), Jernej Ogorevc (Mentor), Jernej Ogorevc (Thesis defence commission member), Minja Zorc (Thesis defence commission member), Polona Jamnik (Thesis defence commission member), Mojca Narat (Thesis defence commission member), Minja Zorc (Co-mentor)

Abstract

CRISPR/Cas tehnologija je relativno enostavna in učinkovita metoda za ciljano urejanje genomov na mestih, ki jih določimo z vodilno RNA (sgRNA). Izbira le-te je poglavitna za zmanjšanje nespecifičnega endonukleaznega delovanja, ki povzroča izven-tarčne učinke. Ker so interakcije med DNA in sgRNA kompleksne, si pri tem pomagamo z algoritmi, ki v genomu izbranega organizma predvidijo potencialna izven-tarčna mesta. V diplomski nalogi smo z algoritmom preverili, če je referenčni genom optimalna izbira za oblikovanje sgRNA pri različnih mišjih linijah. V ta namen smo z algoritmom Cas-OFFinder poiskali izven tarčna mesta za izbrane sgRNA v genomih različnih mišjih linij in v referenčnem genomu miši. Ugotovili smo, da referenčni genom ni vedno optimalna izbira za oblikovanje sgRNA, in da se lahko izven-tarčna mesta pri različnih linijah in celo med posameznimi osebki iste linije razlikujejo. Uporaba referenčnega genoma je torej primerna izbira pri oblikovanju sgRNA za linije, kjer nimamo na voljo specifičnih genomov, a so lahko pri tako oblikovani sgRNA izven-tarčni učinki bolj pogosti kot pri uporabi genoma specifične linije. Optimalna izbira bi bila oblikovanje sgRNA na dejanskem genomu organizma, če to ni mogoče pa na genomu pasem ali linij, ki so našemu organizmu čim bolj sorodni.

Keywords

CRISPR;Cas9;specifičnost;izven-tarčna mesta;

Data

Language: Slovenian
Year of publishing:
Typology: 2.11 - Undergraduate Thesis
Organization: UL BF - Biotechnical Faculty
Publisher: [G. Spruk]
UDC: 575.112(043.2)
COBISS: 9233273 Link will open in a new window
Views: 784
Downloads: 231
Average score: 0 (0 votes)
Metadata: JSON JSON-RDF JSON-LD TURTLE N-TRIPLES XML RDFA MICRODATA DC-XML DC-RDF RDF

Other data

Secondary language: English
Secondary title: Prediction of off-target effects when using CRISPR/Cas9 technology
Secondary abstract: CRISPR/Cas technology is a relatively simple and efficient method for targeted genome editing, directed by single-guide RNAs (sgRNAs). Designing an optimal sgRNA is the key to nonspecific endonuclease activity minimisation, which causes off-target effects. Due to complexity of sgRNA-DNA interactions algorithms are used to predict potential off-target sites in genome of a selected organism. To test, if mouse reference genome is an optimal choice for designing sgRNA in different mouse strains, Cas-OFFinder algorithm was used to predict off-target sites for different sgRNAs, using genomes of different mouse strains and the reference genome. We found that the reference genome is not always an optimal choice for sgRNA design and that off-target sites may differ between mouse strains and even between individuals of the same strain. Use of the reference genome is therefore suitable for sgRNA design in strains where specific genomes are unavailable, but more frequent off-target effects may be observed in such cases. Optimal choice for sgRNA design would be the genome of the targeted organism. In cases when individual genomes are not available, a genome of a closely related breed or strain to the selected organism should be used preferentially to the reference genome.
Secondary keywords: specificity;off-target sites;
Type (COBISS): Bachelor thesis/paper
Study programme: 0
Embargo end date (OpenAIRE): 1970-01-01
Thesis comment: Univ. v Ljubljani, Biotehniška fak., Študij biotehnologije
Pages: VIII, 20 str.
ID: 11149678