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BIOLOGIA MOLECOLARE E BIOLOGIA MOLECOLARE AVANZATA 3
Module ADVANCED MOLECULAR BIOLOGY

Academic Year 2025/2026 - Teacher: ANGELA ANNA MESSINA

Expected Learning Outcomes

Students will be given a clear overview of the molecular mechanisms underpinning the regulation of transcription in the human genome, as well as the role of microRNAs, long non-coding RNAs and methylation in the mechanisms that control biological functions. They will also be provided with knowledge of the experimental tools that have enabled modern advances in scientific research, including technical insights into some of the most widely used methodologies in gene expression analysis. By the end of the course, students will be familiar with and understand the advanced molecular mechanisms regulating transcription in eukaryotes, chromatin modifications and their impact on gene expression, the mechanisms of DNA repair and recombination, the biology of mobile and non-coding genetic elements, the functioning of the silencing system, and the main high-throughput experimental methodologies and bioinformatic analysis techniques.

2. Ability to apply knowledge and understanding (Applying Knowledge and Understanding)

Students will be able to apply the knowledge acquired, interpret the experimental data obtained, and design experimental strategies using the main techniques of advanced molecular biology.

3. Independent judgement (Making Judgements)

Students will be able to critically and independently evaluate scientific literature in the field of advanced molecular biology, formulate interpretative hypotheses based on experimental data, recognise the ethical and biotechnological implications associated with the use of cutting-edge technologies, and express reasoned judgements on the validity and reliability of genomic and transcriptomic data generated by high-throughput approaches.

4. Communication Skills

Students will be able to present the concepts and mechanisms covered in the course clearly and with scientific rigour, both orally and in writing, using technical terminology appropriately and precisely; to discuss the results of a molecular biology experiment in a reasoned manner with both expert and non-expert interlocutors; and to present data and interpretations in a structured manner, for example in response to open-ended questions or during the supplementary oral examination.

5. Learning Skills

Students will have developed the skills necessary to: independently update their knowledge in the field of advanced molecular biology by consulting primary scientific literature; integrate new knowledge with that already acquired in the preparatory courses in Biochemistry and Basic Molecular Biology; and undertake further study programmes requiring advanced skills in functional genomics, epigenetics and translational molecular biology.

Course Structure

Lectures supported by PowerPoint presentations, which will be made available to students on the Studium platform.

The lectures will be supported by classroom-based exercises.

Required Prerequisites

Knowledge of general biochemistry and basic molecular biology.

Attendance of Lessons

Attendance at the course is mandatory to the extent specified in the degree programme rules.

Detailed Course Content

Integration of gene regulation mechanisms in temperate phages. Alternative molecular mechanisms governing the sequence of events that regulate lysis or lysogeny: the action of activators and repressors, retro-regulation and anti-termination. Cloning vectors derived from bacteriophages: insertion vectors, replacement vectors. Transcription regulation in eukaryotes. Control events at the onset of transcription. Regulatory elements on the genome: enhancers, insulators, silencers, functional domains, locus control sequences. Transcription factors. Combinatorial control of transcription. Signal transduction. Chromatin structure and modifications in the regulation of gene transcription. Chromatin modifications: histone modifications, non-allelic histone variants, chromatin remodelling complexes, DNA methylation. DNA repair. Spontaneous or induced mutations and DNA damage. DNA repair pathways: mismatch repair, nucleotide excision repair, base excision repair, direct repair, double-strand break repair, translesion repair. DNA recombination. Homologous recombination: Holliday’s molecular model, the DSB repair model, gene conversion. Site-specific recombination: mechanisms of phage genome integration and excision. Somatic recombination. Non-homologous recombination. Copy-selective recombination (retroviruses). Generation of transgenic organisms. Mobile genetic elements. DNA transposons and mechanisms of replicative and non-replicative transposition. Virus-like/retrovirus-type retrotransposons, poly-A retrotransposons and transposition mechanisms involving RNA intermediates. Pseudogenes. Regulation of translation. Control of ribosome number. Control of translation initiation mediated by CAP, IRES, 5’-3’UTR interactions and riboswitches. Control of mRNA stability via nonsense-mediated decay, no-go decay and non-stop decay. The ENCODE project and the regulation of transcription in the human genome. The importance of rapid, high-throughput NGS sequencing and bioinformatic analysis. Identification of regulatory elements at the genomic and chromatin levels. Methods for studying and analysing chromatin structure and accessibility, epigenetic profiles, transcriptional profiles, and interactions between transcription factors and the genome. Non-coding RNA. lncRNA, siRNA, miRNA and piRNA. Molecular mechanisms of gene silencing and transcriptional regulation mediated by non-coding RNAs. Mechanism of action of the CRISPR-Cas system. Biotechnological applications of regulatory RNAs for the study of gene expression and function.

Textbook Information

Zlatanova & van Holde, Biologia Molecolare: Struttura e dinamica dei Genomi e Proteomi, Zanichelli 2018.

Zlatanova & van Holde, Molecular Biology: Structure and Dynamics of Genomes and Proteomes 2nd Edition CRC Press 2023

Watson, J.D. et al., Biologia Molecolare del gene VIII ed., Zanichelli 2022

Course Planning

 SubjectsText References
1Integration of gene regulation mechanisms into temperate phagesZlatanova & van Holde, Biologia Molecolare: Struttura e dinamica dei Genomi e Proteomi, Zanichelli 2018.Zlatanova & van Holde, Molecular Biology: Structure and Dynamics of Genomes and Proteomes 2nd Edition CRC Press 2023Watson, J.D. et al., Biologia Molecolare del gene VIII ed., Zanichelli 2022
2Transcription regulation in eukaryotesZlatanova & van Holde, Biologia Molecolare: Struttura e dinamica dei Genomi e Proteomi, Zanichelli 2018.Zlatanova & van Holde, Molecular Biology: Structure and Dynamics of Genomes and Proteomes 2nd Edition CRC Press 2023Watson, J.D. et al., Biologia Molecolare del gene VIII ed., Zanichelli 2022
3Chromatin structure and modifications in the regulation of gene transcriptionZlatanova & van Holde, Biologia Molecolare: Struttura e dinamica dei Genomi e Proteomi, Zanichelli 2018.Zlatanova & van Holde, Molecular Biology: Structure and Dynamics of Genomes and Proteomes 2nd Edition CRC Press 2023Watson, J.D. et al., Biologia Molecolare del gene VIII ed., Zanichelli 2022
4DNA repairZlatanova & van Holde, Biologia Molecolare: Struttura e dinamica dei Genomi e Proteomi, Zanichelli 2018.Zlatanova & van Holde, Molecular Biology: Structure and Dynamics of Genomes and Proteomes 2nd Edition CRC Press 2023Watson, J.D. et al., Biologia Molecolare del gene VIII ed., Zanichelli 2022
5DNA recombinationZlatanova & van Holde, Biologia Molecolare: Struttura e dinamica dei Genomi e Proteomi, Zanichelli 2018.Zlatanova & van Holde, Molecular Biology: Structure and Dynamics of Genomes and Proteomes 2nd Edition CRC Press 2023Watson, J.D. et al., Biologia Molecolare del gene VIII ed., Zanichelli 2022
6Mobile genetic elements in DNAZlatanova & van Holde, Biologia Molecolare: Struttura e dinamica dei Genomi e Proteomi, Zanichelli 2018.Zlatanova & van Holde, Molecular Biology: Structure and Dynamics of Genomes and Proteomes 2nd Edition CRC Press 2023Watson, J.D. et al., Biologia Molecolare del gene VIII ed., Zanichelli 2022
7Translation regulationZlatanova & van Holde, Biologia Molecolare: Struttura e dinamica dei Genomi e Proteomi, Zanichelli 2018.Zlatanova & van Holde, Molecular Biology: Structure and Dynamics of Genomes and Proteomes 2nd Edition CRC Press 2023Watson, J.D. et al., Biologia Molecolare del gene VIII ed., Zanichelli 2022
8The ENCODE project and the regulation of transcription in the human genomeZlatanova & van Holde, Biologia Molecolare: Struttura e dinamica dei Genomi e Proteomi, Zanichelli 2018.Zlatanova & van Holde, Molecular Biology: Structure and Dynamics of Genomes and Proteomes 2nd Edition CRC Press 2023Watson, J.D. et al., Biologia Molecolare del gene VIII ed., Zanichelli 2022
9Non-coding RNAZlatanova & van Holde, Biologia Molecolare: Struttura e dinamica dei Genomi e Proteomi, Zanichelli 2018.Zlatanova & van Holde, Molecular Biology: Structure and Dynamics of Genomes and Proteomes 2nd Edition CRC Press 2023Watson, J.D. et al., Biologia Molecolare del gene VIII ed., Zanichelli 2022
10Advanced molecular biology techniquesZlatanova & van Holde, Biologia Molecolare: Struttura e dinamica dei Genomi e Proteomi, Zanichelli 2018.Zlatanova & van Holde, Molecular Biology: Structure and Dynamics of Genomes and Proteomes 2nd Edition CRC Press 2023Watson, J.D. et al., Biologia Molecolare del gene VIII ed., Zanichelli 2022

Learning Assessment

Learning Assessment Procedures

Students who have sat and passed the written examination for the Molecular Biology module (first semester) may sit the written examination for the Advanced Molecular Biology module (second semester). The final mark will be calculated as the average of the marks obtained in the two examinations. A mark of at least 16/30 must be obtained in each examination. The average of the two marks must be at least 18/30. Students who achieve an overall mark of at least 24/30 may sit an oral examination to improve their mark. The mark achieved cannot be reduced as a result of the oral examination.

The written examination consists of 30 multiple-choice questions (+1 mark for a correct answer, 0 marks for an incorrect answer), 1 problem (max 2 marks) and 1 open-ended question (max 2 marks): a total of 34 marks available. 

Students who have not sat or have not passed the written examination for the Molecular Biology module (first semester) may sit a single written examination, for which the minimum mark required to pass is 18/30. Students who achieve an overall mark of at least 24/30 in the examinations may request to sit an oral examination to improve their mark. The mark achieved cannot be reduced as a result of the oral examination.

The single written examination consists of 60 multiple-choice questions (+0.5 for a correct answer, -0.1 for an incorrect answer) + 2 problems (max. 1 mark each) + 2 open-ended questions (max. 1 mark each): a total of 34 marks. Papers in which not a single answer to any of the questions or problems has been provided will not be marked.

Students with specific learning difficulties (SLDs) or certified disabilities that may affect their learning (such as colour blindness, low vision, hearing impairment, dyslexia or physical disabilities) are invited to contact their lecturers to agree on teaching materials and assessment methods.

Assessment may also be carried out online, should circumstances require it.

Examples of frequently asked questions and / or exercises

1. Chromatin immunoprecipitation (ChIP) is used to: a) identify point mutations; b) map DNA-protein binding sites; c) study RNA-RNA interactions; d) analyse transcriptomes; e) quantify total proteins.
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