GENE EXPRESSION AND ANALYSIS TECHNIQUES

Integrated educational activity

Course Sheet

Academic Year of enrolment:

2022/2023

Optional/Mandatory:

Compulsory

Degree:

Master's Degree Programme in BIOLOGY

Language:

Italian

Moduls:

EPIGENETICS, STAMINALITY AND DIFFERENTIATION

5 credits
MOLECULAR BIOTECHNOLOGY IN RESEARCH AND DIAGNOSTICS

5 credits

Credits:

Programme Year:

Hours of classroom activity:

Prerequisites:

Genetics, biochemistry and molecular biology

AF code:

A002917

Assessment Methods

Verification of learning:

Presentation of scientific papers on the topics of the course.
Oral exam aimed at verifying the level of knowledge and depth of the program topics and the reasoning skills developed by the student

Teaching period

First semester

Objectives

The "GENE EXPRESSION AND ANALYSIS TECHNIQUES" course consists of two modules: "EPIGENETICS, STAMINALITY AND DIFFERENTIATION" (5 ECTS) and "MOLECULAR BIOTECHNOLOGIES IN RESEARCH AND DIAGNOSTICS" (5 ECTS), which include lectures, classroom and laboratory actities.

The main objective of the course is to provide the student with knowledge in molecular biology, from the understanding of the mechanisms controlling gene expression in eukaryotic at the transcriptional and post-transcriptional level, to the design of new molecular therapies, such as epigenetic drugs or gene teraphy.
The student will also be competent on the main and most modern experimental technologies for the study of complex biological phenomena. In addition, the course aims to make the student independent in the analysis of experimental data, applying their knowledge, and refine their communication skills, through the analysis and presentation of scientific data in the literature. At the end of the course the student will have the necessary tools to acquire independent judgment.

At the end of the course, the student must demonstrate the following knowledge and skills, consistent with the definition of the profile of the master's degree in Biology (LM6):

1) KNOWLEDGE & UNDERSTANDING
At the end of the lessons and laboratory activities, the student must demonstrate the following skills::
- analyze and discuss topics of regulation of gene expression with mastery;
- propose strategies for investigating gene expression;
- understand and critically analyze the biomolecular literature in all its aspects;
- design detailed experimental approaches on general biomolecular problems.
In particular, the student through lessons, Journal Clubs and practical work, will acquire advanced knowledge on the topics covered in the duration of the course.

2) APPLYING KNOWLEDGE & UNDERSTANDING
The student must also demonstrate the following skills:
- critical analysis for the understanding of concrete biological problems.
- recognize, and autonomously apply, the methodologies necessary for the study of complex biological phenomena
- updating with the consultation of the scientific publications of the disciplinary scientific sector
3) INDIPENDENCE IN JUDGMENT
The student will have to demonstrate autonomy of judgment and evaluation of the experimental results obtained in the laboratory or from the analysis of scientific articles. Team work will be encouraged and promoted via the evaluation of the capacity of sharing competences, discussing criticality and adopting corrective strategies
4) COMMUNICATION SKILLS
Students will be required to demonstrate an adequate technical and scientific lexical richness to expose the experimental results. Team work will be encouraged and promoted via the evaluation of the capacity of sharing competences, discussing criticality and adopting corrective strategies.

Contents

MODULE 1. EPIGENETICS, STAMINALITY AND DIFFERENTIATION (5 ECTS)
LESSONS (4 ECTS):
EPIGENETIC REGULATION OF GENE EXPRESSION
Chromatin structure and organization; ATP-dependent chromatin remodelling systems. DNA methylation. Post-translational modifications of histones: acetylation, phosphorylation and methylation. Histone-modifying enzymes and their structural domains. Heterochromatin and epigenetic regulation of gene expression. Genomic Imprinting. Monoallelic gene expression. Epigenetic control of transposable elements. Role of non-coding RNA in epigenetic modification. Examples: Molecular mechanisms of drugs of abuse and circadian rhythm.

EPIGENETICS, CELL CYCLE AND CANCER
Regulation of gene expression during the cell cycle. The cyclin-kinase complexes and the regulation of their activity. Cell cycle control mechanisms: the role of retinoblastoma and p53 proteins.
Alterations of the cell cycle and epigenetic modifications involved in malignant transformation

LONG TERM REGULATION OF GENE EXPRESSION: DEVELOPMENT AND DIFFERENTIATION
Drosophila to model gene expression regulation during development.
Maternal effect genes that effect the anterior-posterior and the and the dorsal-ventral polarity.
The segmentation genes and the zygotic effect. hunchback a transcriptional repressor. Eve promoter structure.The homeotic genes and the definition of homeotic mutation. The complex antennipedia and bithorax. The homeodomain. the polycomb group proteins and the "freezing of decisions taken".

STEM CELLS: PRINCIPLES AND APPLICATIONS
Biological characteristics of stem cells: definition and characteristics of embryonic, amniotic and adult stem cells. Transcriptional regulation circuits associated with pluripotency: the triad Oct4, Nanog and Sox2; the polycomb group proteins and the chromatinic structure. Epigenetic modifications and cell identity in stem cells. Nuclear reprogramming and pluripotency induction methods (iPS). Applications of iPS. Tumor stem cells: biomolecular characteristics. Therapeutic potential of stem cells.

EPIGENETICS and NUTRITION
Principles and examples

LABORATORY (1 ECTS):
ChIP Analysis of c-fos promoter in human cells upon stimulation with serum.

MODULE 2. TECHNIQUES OF ANALYSIS OR MANIPULATION OF GENE EXPRESSION (5 ECTS)
LESSONS (4 ECTS):
Basic techniques in the study of gene function. Gene targeting 1.0: Genetic manipulation in animals. Transgenic mice. Site-specific recombination and inducible knock-out mice. Gene targeting 2.0: Genome-editing nuclease: ZFN, TALEN, CRISPR-Cas9. Application of the different techniques in the analysis or manipulation of gene expression.

RNA INTERFERENCE AND THERAPEUTIC RNA
RNA interference and non-coding RNA: miRNA, snoRNA, lncRNA and circRNA. Attamers. RNA splicing modifiers. Technology antimiR.

GENE THERAPY: PRINCIPLES AND APPLICATIONS
Analysis of the different viruses utilized for gene therapy: adenovirus. adeno-associated virus, retrovirus and lentivirus. Advantages and disadvantages of the different virus. Examples of gene therapy in the treatment of different human diseases.

PRECISION MEDICINE FOR NEW DIAGNOSTIC AND THERAPEUTIC APPROACHES.
General concepts. Examples of precision medicine in the treatment of different human diseases: Antibody therapies and T-CART therapy.

LABORATORY (1 ECTS):
molecular biology techniques

Recommended Bibliography

1) L. Armstrong "Epigenetics" Garland Science
2) Epigenetics © 2006 Cold Spring Harbor Laboratory Press
3) Molecular Biology of the Gene- Watson et al.,
4) Extra reading material - a list of review articles
5) The slides and other materials used for lectures is made available to the students on the online moodle platform.

Methods of Provision

Conventional

Teaching Methods

Lectures, using slides and video. Theoretical and practical exercises. Journal Club

Contacts/More Information

1) Readiness to offer individual assistance also in English language to incoming students
2) Availability of supporting material and bibliographic references in English.
List:.Epigenetics. Allis, Jenuwein, Reinberg and Caparros. Cold Spring Harbour Laboratory Press. ISBN-13:978-0879697242
3) Readiness to accept examination of incoming students also in a English

GENE EXPRESSION AND ANALYSIS TECHNIQUES

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GENE EXPRESSION AND ANALYSIS TECHNIQUES