Course Details

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Course Information
SemesterCourse Unit CodeCourse Unit TitleT+P+LCreditNumber of ECTS CreditsLast Updated Date
1BENG549GENOME EDITING: CRISPR3+0+037,515.05.2025

 
Course Details
Language of Instruction English
Level of Course Unit Master's Degree
Department / Program BIOENGINEERING
Type of Program Formal Education
Type of Course Unit Elective
Course Delivery Method Face To Face
Objectives of the Course This course aims to introduce students to the field of genome editing technologies. Students will explore the historical development of genome editing tools including Zinc Finger Nucleases (ZNF), Transcription Activator-Like Effector Nucleases (TALEN), and CRISPR/Cas9. The course will provide an in-depth understanding of CRISPR experimental design including sgRNA selection, vector-based and vector-free systems, screening strategies, efficiency, specificity, and safety. The role of CRISPR-based genome editing in treating cancer and monogenic diseases will be discussed, alongside its ethical implications.
Course Content The course will begin with the historical development and comparison of genome editing technologies such as ZNF, TALEN, and CRISPR/Cas9. It will then cover CRISPR experimental design strategies including target site selection, sgRNA design, vector-based and vector-free delivery systems, screening approaches, and methods to evaluate efficiency, specificity, and safety. Students will learn about the therapeutic applications of CRISPR/Cas9 in treating cancer and monogenic diseases, and how it is used to dissect gene functions. The course will conclude with a discussion on the ethical dimensions of genome editing.
Course Methods and Techniques The course will employ lectures, literature review, case studies, group discussions, and debates on ethical dilemmas. Students will also design mock CRISPR experiments and analyze scientific publications related to genome editing.
Prerequisites and co-requisities None
Course Coordinator None
Name of Lecturers Associate Prof.Dr. Oktay İ. Kaplan oktay.kaplan@agu.edu.tr
Assistants None
Work Placement(s) No

Recommended or Required Reading
Resources Ceccaldi, R., Rondinelli, B., & D’Andrea, A. D. (2016). Repair pathway choices and consequences at the double-strand break. Nature Reviews Molecular Cell Biology, 17, 5–18.
Chang, H. H. Y. et al. (2017). Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nature Reviews Molecular Cell Biology, 18, 495–506.
Komor, A. C., Badran, A. H., & Liu, D. R. (2017). CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes. Cell, 168(1–2), 20–36.
Qi, L. S., et al. (2013). Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell, 152(5), 1173–1183.
Anzalone, A. V., Koblan, L. W., & Liu, D. R. (2020). Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors. Nature Biotechnology, 38, 824–844.
Liu, Y. et al. (2020). Optimizing prime editing by maximizing pegRNA efficiency and minimizing indels. Nature Biotechnology
Dever, D. P. et al. (2016). CRISPR/Cas9 ß-globin gene targeting in human haematopoietic stem cells. Nature, 539, 384–389.
Esrick, E. B., & Williams, D. A. (2020). Safety and efficacy of gene therapy for ß-thalassemia and sickle cell disease. Blood, 136(3), 273–282.
Regalado, A. (2018). The CRISPR baby scandal gets worse by the day. MIT Technology Review
Course Notes What is genome editing?

Early gene-editing tools: ZFNs and TALENs

Discovery and development of CRISPR-Cas systems

Milestones in CRISPR history (Doudna & Charpentier, Zhang lab)
Documents nope
Assignments Nope
Exams Nope

Course Category
Mathematics and Basic Sciences %50
Engineering %0
Engineering Design %0
Social Sciences %0
Education %0
Science %0
Health %50
Field %0

Planned Learning Activities and Teaching Methods
Activities are given in detail in the section of "Assessment Methods and Criteria" and "Workload Calculation"

Assessment Methods and Criteria
Veri yok

 
ECTS Allocated Based on Student Workload
Activities Quantity Duration Total Work Load
Deney 1 80 80
Proje 1 150 150
Total Work Load   Number of ECTS Credits 7,5 230

 
Course Learning Outcomes: Upon the successful completion of this course, students will be able to:
NoLearning Outcomes
1 Describe Genome Editing History: ZNF and TALEN and, CRISPR.
2 Apply CRISPR design; CRISPR-mediated genome editing and human diseases.
3 Interpret CRISPR-based Functional Analysis of Genes and CRISPR/Cas9 for Human Therapeutics.
4 Define Cas9 like enzymes, and CRISPR Techniques with the ethics.

 
Weekly Detailed Course Contents
WeekTopicsStudy MaterialsMaterials
1 Introduction & History of CRISPR Molecular Mechanism of CRISPR-Cas9 DNA Repair and CRISPR Mechanisms Genome Editing Applications CRISPR-based Gene Regulation (CRISPRi/a) New Tools: Base Editing, Prime Editing Clinical Applications & CRISPR Therapeutics CRISPR Experimental Design and Bioinformatics Ethics and Biosafety Week 1 Doudna & Charpentier (2012). The new frontier of genome engineering with CRISPR-Cas9. YouTube Documentary: "The Gene: An Intimate History" (CRISPR segment) Week 2 Hsu, Patrick D. et al. (2014). Development and Applications of CRISPR-Cas9 for Genome Engineering. Cell, 157(6), 1262-1278. Week 3 Review article on DNA repair mechanisms (NHEJ and HDR): e.g., Scully et al. (2019). DNA double-strand break repair-pathway choice in somatic mammalian cells. Nature Reviews Molecular Cell Biology. Week 4 Application-focused papers: e.g., Mali et al. (2013). RNA-guided human genome engineering via Cas9. Science. Week 5 Gilbert et al. (2013). CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell. Week 6 Anzalone et al. (2019). Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. Week 7 Frangoul et al. (2021). CRISPR-Cas9 gene editing for sickle cell disease and ß-thalassemia. NEJM. Week 8 Articles and editorials abou Week 1 Doudna & Charpentier (2012). The new frontier of genome engineering with CRISPR-Cas9. YouTube Documentary: "The Gene: An Intimate History" (CRISPR segment) Week 2 Hsu, Patrick D. et al. (2014). Development and Applications of CRISPR-Cas9 for Genome Engineering. Cell, 157(6), 1262-1278. Week 3 Review article on DNA repair mechanisms (NHEJ and HDR): e.g., Scully et al. (2019). DNA double-strand break repair-pathway choice in somatic mammalian cells. Nature Reviews Molecular Cell Biology. Week 4 Application-focused papers: e.g., Mali et al. (2013). RNA-guided human genome engineering via Cas9. Science. Week 5 Gilbert et al. (2013). CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell. Week 6 Anzalone et al. (2019). Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. Week 7 Frangoul et al. (2021). CRISPR-Cas9 gene editing for sickle cell disease and ß-thalassemia. NEJM. Week 8 Articles and editorials abou

 
Contribution of Learning Outcomes to Programme Outcomes
P1 P2 P3 P4 P5 P6 P7 P8 P9 P10 P11 P12
All 4 5 3 5 3 4 2 5 5 4 1 4
C1 4 5 3 4 3 4 1 4 4 5 1 3
C2 4 5 3 5 3 4 2 4 3 5 2 2
C3 3 5 3 5 3 3 3 3 4 3 1 3
C4 3 5 3 3 2 3 1 3 4 5 1 2

  Contribution: 1: Very Slight 2:Slight 3:Moderate 4:Significant 5:Very Significant

  
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