B6302 - MOLECULAR BASIS OF GENOME EDITING

Learning outcomes

At the end of the course, the student possesses in-depth knowledge of the molecular mechanisms underlying genome editing methodologies in eukaryotic and prokaryotic cells and the main applications in biotechnology. In particular, the student is able to: 1) analyze and discuss topics concerning the basic mechanisms and applications of these methodologies; 2) understand and critically analyze the biomolecular literature.

Course contents

Introduction to basic concepts concerning nucleic acids in the cell. Chemical structure of nucleic acids. Physical structures of DNA and RNA molecules. Genetic code, genes and genomes. Physical structure of genetic material: bacterial chromosomes (chromatin), eukaryotic chromatin, higher order chromatin structures.

DNA recombination. Biological role of homologous recombination. Molecular mechanisms of homologous recombination in bacterial cells and in eukaryotic cells. Non-homologous recombination. Site-specific recombination.

Mechanisms of DNA repair. Types of DNA lesions. Pathways and mechanisms of DNA repair: DNA photolyase, Nucleotide Excision Repair, Base Excision Repair, Mismatch Repair. Repair mechanisms of DNA double-strand breaks: Nonhomologous end-joining and homologous recombination repair.

Conventional approaches used for genome-editing: homologous recombination, chemical methods and approaches based on homing endonucleases.

Genome-editing approaches based on modern methodologies using sequence-specific all-protein nucleases: mega-nucleases, zinc-finger nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs).

Genome-editing approaches based on methodologies using RNA-guided nucleases: Clustered regularly interspaced short palindromic repeats (CRISPR-CAS systems).

Examples of applications of the various systems in different fields.

Laboratory part: the course includes an individual laboratory activity where the CRISPR-Cas9 system is used to specifically target and cleave a gene sequence of interest. The aim is to evaluate how introduced mutations affect target recognition and cleavage efficiency by the endonuclease.

Readings/Bibliography

Zlatanova, Jordanka, Kensal E. Holde. Molecular Biology, 2nd Edition. Garland Science, 20230421. VitalBook file.

Reviews and seminal papers.

Teaching methods

The course includes:

• lectures with PowerPoint presentations to introduce and explain theoretical content;
• guided classroom discussions on scientific articles and case studies;
• group work and interactive activities using innovative teaching tools;
• individual workstation laboratory exercises focused on CRISPR-Cas system applications.
  

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 on-site and consists of an oral interview with three questions covering different parts of the course content. Each answer will be assessed based on completeness, scientific accuracy, clarity of presentation, and ability to connect topics, in line with the expected learning outcomes.

The exam aims to assess:

• theoretical understanding of the molecular basis of genome editing techniques,
• ability to apply knowledge to real-world cases and applications,
• autonomy of judgment in critically discussing the topics covered,
• communication skills in presenting content.

Formative assessment: discussion sessions, exercises, and feedback moments are planned during the course to help monitor learning progress; however, they do not contribute to the final grade.

The criteria used to assess the acquisition of knowledge and competencies are:

1. understanding of the topics;
2. completeness of acquired knowledge;
3. use of appropriate language during oral presentation and ability to synthesize concepts;

ability to make connections between the various topics covered.

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

For students attending the course, all materials used for the lectures (ppt presentations, articles/reviews and book chapters/monographs) and for laboratory activities (presentation of exercises and related handouts) will be made available.

Office hours

See the website of Davide Roncarati