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

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.

Readings/Bibliography

Reviews and seminal papers.

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 exam takes place in person and consists of an oral interview covering different parts of the course program. The exam is designed to assess the achievement of the main learning objectives:

1. the ability to analyze and confidently discuss topics related to the mechanisms underlying CRISPR-Cas systems and their applications;

2. the ability to critically understand and analyze biomolecular literature in all its aspects;

3. the ability to design detailed experimental approaches to general biomolecular problems.

The assessment consists of two parts:

• Part one involves the in-class presentation of a scientific article exploring a topic covered during the course (this assesses learning objective 2; max score: 10 points).

• Part two is an oral interview based on two questions related to different areas of the course content (this assesses learning objectives 1 and 3; max score: 20 points). For each question, the student is assigned a score based on their ability to clearly and concisely present the relevant topics, including elements of critical analysis.

The final grade, expressed in thirtieths, is determined by the combined scores from the oral presentation of the scientific article and the oral interview.

The criteria used to evaluate the acquisition of knowledge and skills include:

1. understanding of the topics;

2. completeness of the acquired knowledge;

3. use of appropriate language during oral communication and ability to summarize key concepts;

4. ability to make connections between the various topics covered in the course.

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

Reviews and seminal research papers. PowerPoint presentations. Registered students can download lesson presentations, articles and other teaching materials through the Insegnamenti Online website: https://virtuale.unibo.it

Office hours

See the website of Davide Roncarati