96032 - Crispr-Cas Systems: from Bacterial Adaptive Immunity to Genome-Editing Applications

Learning outcomes

The student will gain in depth knowledge of the molecular mechanisms governing adaptation, expression and interference of the major CRISPR/Cas bacterial immunity systems; of the CRISPR/Cas-based methodologies used for genome editing and gene-expression modulation; of the main CRISPR/CAS-based biotechnological applications. In particular, at the end of the course, the student will be able to: - analyse and discuss the main topics concerning CRISPR/Cas mechanisms and applications; - understand, analyse and discuss research papers; - plan experimental approaches to study a biological problem.

Course contents

The course provides an in-depth overview of CRISPR-Cas systems, from their biological role as adaptive immune systems in bacteria and archaea to their revolutionary applications in genome engineering, biotechnology and medicine.

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

The course covers the following topics:

CRISPR-Cas Systems in Their Natural Biological Context

• From the earliest observations to the characterization of CRISPR-Cas systems as adaptive and heritable immune mechanisms in prokaryotes.

• Structure and classification of CRISPR-Cas systems: general features and key components; classification and complexity of the various CRISPR systems identified in nature.

• The phases of CRISPR-Cas immunity: acquisition of new spacers, expression of the CRISPR locus, maturation of the precursor transcript, and the interference mechanism.

• Interference mechanisms: detailed description of the functioning of the most studied systems—Cas9, Cas12, Cas13, and Cascade-Cas3.

• Discrimination between self and non-self DNA: major molecular mechanisms that allow CRISPR systems to distinguish endogenous from exogenous DNA.

Biotechnological Applications of CRISPR-Cas Systems

• Gene editing via double-strand breaks (DSBs): techniques based on DNA repair pathways such as Non-Homologous End Joining (NHEJ), Microhomology-Mediated End Joining (MMEJ), and Homology-Directed Repair (HDR).

• Comparison with other genome editing technologies, such as Zinc-Finger Nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs).

• Gene editing without DSBs: technologies based on base editors and prime editors.

• Gene expression modulation: use of CRISPRi and CRISPRa systems in prokaryotic and eukaryotic organisms; introduction to epigenetic engineering technology (CRISPRoff).

• Other applications in the biotechnological field.

• Ethical considerations: ethical implications related to the use of CRISPR-Cas technologies, particularly in the context of human genome editing.

The course includes the critical analysis and discussion of landmark and recent scientific papers.

Throughout the course, students will strengthen transversal skills including critical analysis of scientific literature, scientific communication, experimental design, teamwork and critical discussion.

Readings/Bibliography

Study materials consist of review articles, landmark research papers and additional scientific literature selected by the instructor and made available through the Virtuale platform.

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

Additional references for further reading may be suggested during the course.

Teaching methods

The course includes:

• Lectures supported by PowerPoint presentations, aimed at introducing and explaining theoretical content;

• Guided in-class discussions on scientific articles and case studies;

• Group work and interactive activities based on innovative teaching tools.

In addition to contacting the course instructor, students with disabilities, specific learning disorders (DSA), special educational needs (BES), or other health conditions may also reach out to ASES - Right to Higher Education Unit - service for students with disabilities and SLD to receive more information about available teaching support and specific tools.

Assessment methods

The final assessment consists of a single on-site oral examination comprising two complementary components, designed to evaluate the achievement of the intended learning outcomes.

The first component consists of the preparation, presentation and classroom discussion of a scientific paper selected in agreement with the instructor and related to one of the topics covered during the course. This component contributes one third of the final grade (up to 10 points) and is designed to assess:

• the ability to critically analyse the scientific literature;
• the ability to interpret experimental results;
• scientific communication and presentation skills.

The second component consists of an oral examination including two questions covering different sections of the course syllabus. This component contributes two thirds of the final grade (up to 20 points) and is designed to assess:

• understanding of the biology of CRISPR-Cas systems and genome-editing technologies;
• the ability to critically discuss the molecular mechanisms, applications, limitations and future perspectives of CRISPR technologies;
• the ability to design and discuss appropriate experimental approaches to address biomolecular research questions;
• the use of appropriate scientific terminology and the ability to integrate concepts across the different topics covered during the course.

The final mark (out of 30) is obtained by combining the scores achieved in the two assessment components.

Final grades are awarded according to the following criteria:

• 18–21: sufficient knowledge of the main topics, with limited critical analysis and limited ability to integrate concepts.
• 22–25: good knowledge of the course contents, appropriate scientific language and satisfactory critical reasoning.
• 26–29: very good understanding of the subject, ability to critically analyse the scientific literature, independently discuss experimental approaches and establish connections among different course topics.
• 30–30L: comprehensive knowledge of all course topics, excellent critical thinking, ability to integrate concepts across different areas, outstanding scientific communication and independent scientific reasoning.

No written assignments are required before the examination.

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., literature summarization, concept clarification or self-assessment).

During the assessment, any substantial use of generative AI for preparing the presentation or answering examination questions 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, which must be approved by the instructor 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

Teaching materials include:

• PowerPoint presentations;
• review articles;
• landmark and recent scientific papers;
• supplementary reading material;
• multimedia resources;
• material uploaded on the 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