B6302 - MOLECULAR BASIS OF GENOME EDITING

Learning outcomes

The student will gain in-depth knowledge of the molecular mechanisms underlying DNA recombination, DNA repair and genome editing, as well as of the principles, applications and limitations of the major genome-editing technologies currently employed in basic research, biotechnology and biomedicine. Through the laboratory activities, the student will also acquire practical knowledge of CRISPR-Cas9-mediated genome editing and of the experimental approaches used to analyse genome-editing outcomes.

In particular, at the end of the course, the student will be able to:

• analyse and discuss the molecular mechanisms underlying DNA recombination, DNA repair and genome-editing technologies;
• critically compare conventional and modern genome-editing approaches, including programmable nucleases and CRISPR-Cas systems;
• understand, analyse and critically discuss scientific literature in the field of genome editing;
• design appropriate experimental strategies to address biological questions using genome-editing technologies;
• interpret and critically evaluate experimental results obtained from genome-editing experiments.

Course contents

The course provides the theoretical and practical foundations of genome editing technologies, introducing the molecular mechanisms that underlie DNA recombination, DNA repair and targeted genome modification.

Recommended prerequisites: a basic knowledge of molecular biology, genetics and gene expression is recommended.

The course covers the following topics:

Module 1

• Introduction to nucleic acids: chemical structure of DNA and RNA, physical organization of nucleic acids, genetic code, genes and genomes, bacterial chromosomes and eukaryotic chromatin organization.
• DNA recombination: biological significance of homologous recombination; molecular mechanisms of homologous recombination in bacteria and eukaryotes; non-homologous and site-specific recombination.
• DNA damage and repair: types of DNA lesions and major repair pathways, including photoreactivation, nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), non-homologous end joining (NHEJ) and homologous recombination repair (HR).

Module 2

• Conventional genome-editing approaches based on homologous recombination, chemical mutagenesis and homing endonucleases.
• Protein-based programmable nucleases: meganucleases, Zinc Finger Nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs).
• RNA-guided genome-editing technologies based on CRISPR-Cas systems.
• Current and emerging applications of genome-editing technologies in biotechnology, biomedicine and basic research.

Laboratory activities

The course includes an individual laboratory experience in which students perform targeted cleavage of a selected DNA sequence using the CRISPR-Cas9 system. Students will evaluate how sequence modifications influence target recognition and nuclease cleavage efficiency, gaining practical experience in experimental design, data interpretation and critical analysis of genome-editing strategies.

Throughout the course, students will also develop transversal competences including critical analysis of scientific literature, scientific communication, experimental design, teamwork and problem-solving.

Readings/Bibliography

Required study materials include:

• Zlatanova J., van Holde K. Molecular Biology, 2nd Edition. Garland Science.
• Review articles and selected landmark research papers provided by the instructor through the University’s Virtuale platform.

PowerPoint presentations used during lectures and laboratory sessions are provided as study support but do not replace the assigned scientific literature.

Additional references may be suggested during the course for students wishing to further explore specific topics.

Teaching methods

The course is organized into two lecture modules (5 ECTS), covering the theoretical foundations and molecular mechanisms of genome editing, and one laboratory module (2 ECTS), consisting of 32 hours of individual hands-on practical sessions conducted in a single-workstation laboratory. During the laboratory activities, each student will independently carry out the entire experimental workflow, from experimental setup to data analysis and interpretation of the results.

Teaching activities include:

• lectures supported by PowerPoint presentations introducing theoretical concepts;
• guided discussion of scientific papers and case studies;
• group work and interactive classroom activities based on active-learning approaches;
• individual laboratory sessions focused on CRISPR-Cas genome editing;
• discussion of experimental results and troubleshooting strategies.

Teaching materials will be made available through the University’s Virtuale platform.

Because the course includes laboratory activities, students are required to comply with the University safety regulations and complete any mandatory safety training required by the Degree Programme before accessing the laboratory.

Students with disabilities, specific learning disorders (DSA), special educational needs (BES) or other health conditions may contact the University’s disability and inclusion services to discuss available support measures.

Assessment methods

The final assessment consists of a single on-site oral examination covering all course modules. The examination includes three questions, each addressing one of the three components of the course:

• one question on the theoretical contents covered in Module 1;
• one question on the theoretical contents covered in Module 2;
• one question on the laboratory module, aimed at assessing the student’s understanding of the experimental activities, methodologies and interpretation of the results.

The examination is designed to evaluate the achievement of the intended learning outcomes, including:

• understanding of the molecular basis of genome-editing technologies;
• ability to apply theoretical knowledge to experimental and real-world scenarios;
• critical discussion of genome-editing methodologies and applications;
• use of appropriate scientific terminology and communication skills.

Formative assessment is carried out during the course through guided discussions, classroom exercises and feedback sessions. These activities do not contribute to the final grade.

Final grades are awarded according to the following criteria:

• 18–21: sufficient understanding of the main concepts, with limited ability to integrate topics and discuss them critically.
• 22–25: good knowledge of the course contents, appropriate scientific language and satisfactory analytical skills.
• 26–29: very good understanding of genome-editing technologies, ability to critically analyse methodologies and discuss applications independently.
• 30–30L: comprehensive knowledge of all course topics, excellent critical thinking, integration of concepts, scientific accuracy and outstanding communication skills.

During the oral examination, the use of books, notes, electronic devices or any other supporting material is not permitted.

Generative AI tools may be used only as support for individual study activities (e.g. summarizing literature, clarifying concepts or self-assessment). Their substantial use during the preparation of examination answers is not permitted. Limited use for language revision or formatting is acceptable only if explicitly declared by the student. Undeclared or substantial use of generative AI constitutes a violation of academic integrity.

Students with disabilities or specific learning disorders (DSA) are encouraged to contact the University’s dedicated office well in advance to discuss possible accommodations, in accordance with University regulations.

Students with learning disorders and\or temporary or permanent disabilities: please, contact the office responsible ( https://site.unibo.it/studenti-con-disabilita-e-dsa/en ) as soon as possible so that they can propose acceptable adjustments. The request for adaptation must be submitted in advance (15 days before the exam date) to the lecturer, who will assess the appropriateness of the adjustments, taking into account the teaching objectives.

Students recognized as “working students”
Please consult the dedicated website ( https://www.unibo.it/en/study/guide-to-choosing-your-programme/balancing-study-and-work ) to apply for this status and to learn about the available measures.

Teaching tools

Students attending the course will receive:

• PowerPoint presentations used during lectures;
• laboratory protocols and supporting handouts;
• review articles and landmark scientific papers;
• book chapters and additional reading materials;
• supplementary teaching resources uploaded to the University’s Virtuale platform.

Students are encouraged to use digital resources, including generative AI tools, critically and responsibly as support for individual learning, always verifying information against primary scientific literature.

Office hours

See the website of Davide Roncarati

See the website of Giulia Miglietta