Learning objectives
The aim is to provide an in-depth knowledge on the mechanisms controlling eukaryotic gene expression at both the transcriptional and post-transcriptional level, taking into account the information recently made available by genomics. This will be pursued through a unifying conceptual framework pointing to general regulatory strategies shared by prokaryotes and eukaryotes and by different phases of the genetic information transfer process (transcription, mRNA splicing and other post-transcriptional events, controlled modification/degradation and subcellular localization of proteins, signal transduction to the cell nucleus). Both theoretical and practical aspects of gene expression control will be considered, with special emphasis on its biomedical and molecular diagnostics applications/implications.
Prerequisites
Basic knowledge in chemistry, biochemistry, molecular biology and genetics.
Course unit content
Content of Eukaryotic genomes.
Processes based on "regulated recruitment".
Eukaryotic RNA polymerases, general transcription factors and regulatory cis elements.
Nucleosomes, chromatin and higher-order chromatin structures.
Transcriptional and post-transcriptional regulation.
Introduction to the cross-talk metabolism-gene regulation.
Signal transduction with emphasis on the nuclear processes.
Full programme
Contenuto del Genoma ed Elementi Trasponibili.
Reclutamento regolato.
Fattori di trascrizione e il dominio di attivazione (AD).
RNA polimerasi eucariotiche (RNA pol I, pol II, pol III, e accenno alle pol IV e V).
Fattori Generali della Trascrizione (GTFs), il Mediatore e sequenze in cis (TATA, BRE, DPE, enhancers, etc.).
Trascrizione specifica e tecniche per analisi di promotori e fattori di trascrizione. Trascrizione bidirezionale.
Cromatina, nucleosomi e istoni con varianti e modificazioni post-traduzionali (PTMs). Organizzazione nucleare della cromatina. Epigenetica e metilazione del DNA.
Trascrizione di un gene codificante e modificazioni co-/post-trascrizionali: CAPping, Cleavage/polyA e Terminazione.
Pre-mRNA splicing e alternative splicing.
Regolazione della stabilità del trascritto, controllo di qualità ed export nucleare.
Introduzione al cross-talk fra metabolismo e regolazione genica.
Long non-coding RNAs.
Ubiquitina: controllo stabilità proteica e modificazione post-traduzionale.
Esempi di regolazione in lievito (mating type switch, ciclo cellulare, eterocromatina telomerica).
Esempi di trasduzione del segnale (Unfolded Protein Response; heat-shock; cholesterol sensing; Notch/Delta, APP, SynNotch; NF-κB; Wnt/β-catenin; Nuclear Receptors; GPCRs; TGF-β/Smad; RTKs)
Seminari (in inglese) - Articoli selezionati dalla letteratura
Contenuto del Genoma ed Elementi Trasponibili.
Reclutamento regolato.
Fattori di trascrizione e il dominio di attivazione (AD).
RNA polimerasi eucariotiche (RNA pol I, pol II, pol III, e accenno alle pol IV e V).
Fattori Generali della Trascrizione (GTFs), il Mediatore e sequenze in cis (TATA, BRE, DPE, enhancers, etc.).
Trascrizione specifica e tecniche per analisi di promotori e fattori di trascrizione. Trascrizione bidirezionale.
Cromatina, nucleosom, istoni e modificazioni post-traduzionali (PTMs). Organizzazione nucleare della cromatina.
Epigenetica e metilazione del DNA.
Trascrizione di un gene codificante e modificazioni co-/post-trascrizionali: CAPping, Cleavage/polyA e Terminazione.
Pre-mRNA splicing e alternative splicing.
Regolazione della stabilità del trascritto, controllo di qualità ed export nucleare.
Introduzione al cross-talk fra metabolismo e regolazione genica.
Long non-coding RNAs.
Ubiquitina: controllo stabilità proteica e modificazione post-traduzionale.
Esempi di regolazione in lievito (mating type switch, ciclo cellulare, eterocromatina telomerica).
Esempi di trasduzione del segnale (Unfolded Protein Response; heat-shock; cholesterol sensing; Notch/Delta, APP, SynNotch; NF-κB; Wnt/β-catenin; Nuclear Receptors; GPCRs; TGF-β/Smad; RTKs)
Seminari (in inglese) - Articoli selezionati dalla letteratura
Genome content and transposable elements
Regulated recruitment
Transcription factors and the activation domain (AD)
Eukaryotic RNA polymerases (RNA pol I, pol II, pol III, and brief mention to pol IV and pol V)
General transcription factors (GTFs), Mediator, cis DNA elements (TATA, BRE, DPE, enhancers, etc.)
Specific transcription and techniques to study promoters and transcription factors. Bidirectional transcription.
Chromatin, nucleosomes, histones, and post-translational modifications (PTMs). Nuclear chromatin organization.
Epigenetics and DNA methylation.
Transcription of a coding gene and co-/post-transcriptional processing: CAPping, Cleavage/polyA and Trascriptional Termination.
Pre-mRNA splicing and alternative splicing.
Transcript stability regulation, quality control and nuclear export.
Introduction of metabolism-gene regulation cross-talk.
Long non-coding RNAs.
Ubiquitin: from PTM to control of the protein stability.
Examples of gene/protein activity regulation in yeast (mating type switch, cell cycle, telomeric heterochromatin)
Examples of signal transduction (Unfolded Protein Response; heat-shock; cholesterol sensing; Notch/Delta, APP, SynNotch; NF-κB; Wnt/β-catenin; Nuclear Receptors; GPCRs; TGF-β/Smad; RTKs)
Seminar-style lectures (in English) - from scientific literature
Bibliography
Harvey Lodish; Arnold Berk; Chris A. Kaiser; Monty Krieger; Anthony Bretscher; Hidde Ploegh; Kelsey C. Martin; Michael Yaffe; Angelika Amon
MOLECULAR BIOLOGY OF THE CELL (9th Edition - 2021) Macmillan Higher-Education
Watson J.D., Backer T.A., Bell S. P., Gann A., Levine M., Losick R. a cura di Paolo Plevani
BIOLOGIA MOLECOLARE DEL GENE/MOLECULAR BIOLOGY OF THE GENE
(Edizione VIII - 2022) Zanichelli
Ptashne M., Gann A.
GENES and SIGNALS
(2002) COLD SPRING HARBOR LABORATORY PRESS
Craig, N., Green, R., Greider, C., Storz, G. and Wolberger, C.
Molecular Biology: Principles of Genome Function.
(3rd Edition - 2021). Oxford University Press Academic UK
Jordanka Zlatanova, Kensal E. van Holde, a cura di Vito De Pinto
Biologia molecolare - Struttura e dinamica di genomi e proteomi
(1st Edition - 2018) Zanichelli
Francesco Amaldi, Piero Benedetti, Graziano Pesole, Paolo Plevani
Biologia molecolare.
(3rd Edition - 2018) Casa Editrice Ambrosiana/Zanichelli
Scientific Papers (English)
Lecture slides (pdf)
Teaching methods
The course is mainly based on lectures, but it also includes critical reading of scientific literature and visualization/analysis of experimental data.
Some lectures will be held in English (seminar style).
Assessment methods and criteria
The evaluation of the expected learning achievements will be based on an oral examination that will also include the discussion of specific regulatory schemes, application examples/case-studies presented in the course. Moreover, the ability to apply methodologies and contents from the course to solve experimental problems will be tested. This will allow a detailed evaluation of the theoretical and practical knowledge on the various genetic information transfer/elaboration processes illustrated in the course as well as the ability to apply such knowledge to address and solve specific experimental problems.
Other information
Students are expected to acquire a detailed knowledge of some of the most important cellular and molecular processes underlying the elaboration of eukaryotic genome information and related applications, especially with regard to bio/molecular medicine. Special emphasis will be placed on post-genomic experimental strategies that are being employed to discover and/or functionally characterize novel bio-active compounds.
APPLYING KNOWLEDGE AND UNDERSTANDING. Through the guided analysis of key experiments that have allowed to understand some of the above described processes, students will acquire the basic knowledge and competence required for the study of genetic information transfer/elaboration processes at the molecular level and for the exploitation of genomics as a tool for the functional characterization of bio-active small-molecules and the identification of novel compounds.
