C8701 - FUNCTIONAL GENETICS AND INTEGRATIVE GENOMICS

Learning outcomes

"At the end of the course the student: • understands the principles of functional genomics and integrative approaches to study gene regulation, expression, and interaction networks; • is able to critically analyze how genetic modification (knockout, knockdown, overexpression, CRISPR-based editing) affect cellular and organismal phenotypes; • functional dissection of biological processes of interest using animal model systems • acquires familiarity with large-scale genomic datasets (transcriptomics, epigenomics, proteomics) and how to integrate them for functional insights; • develops the ability to interpret results from genome-wide association studies (GWAS) and functional validation pipelines; • gains skills to apply bioinformatics tools and integrative analysis frameworks in order to connect genotype with phenotype in biomedical and biotechnological contexts. "

Course contents

Prerequistes of the course are general notions of Biochemistry, Molecular Biology and Genetics.

Module of Functional Genetics

Lecture 1 Introduction to Functional Genetcs/Genomics (Concept of gene function and genetic perturbations).

Lectures 2-3 Main genetic model systems:unicellular: Saccharomyces cerevisiae;

Lectures 4-5 Invertebrates:Caenorhabditis elegans, Drosophila melanogaster

Lectures 6-8 Vertebrates: Danio rerio, Mus musculus) and their peculiar methods and use to perform genetic screens alchilant or insertional (retroviral vectors, transposons) mutagenesis.

Lectures 9-10 Genetic Manipulation Technologies (RNAi, CRISPR-Cas9, transposon mutagenesis, Conditional and tissue-specific gene perturbations.

Module of Integrative genomics

Lecture 1-2 introduce the rationale for integrative genomics, explaining why biological complexity cannot be understood from a single omics layer alone.

Lecture 3-4 focus on omics technologies and experimental design, including WGS, WES, RNA-seq, ATAC-seq, ChIP-seq, DNA methylation, proteomics, metabolomics, single-cell, and spatial omics.

Lectures 5-6 explore gene regulation by integrating genomics, epigenomics, and transcriptomics, with emphasis on promoters, enhancers, chromatin accessibility, transcription factor binding, DNA methylation, enhancer–gene linking, motif analysis, and regulatory networks.

Lecture 7-8 focus on pathway and network biology, including pathway enrichment, GSEA, protein–protein interaction networks, disease modules, causal networks, and master regulators. We will examine single-cell integrative genomics, including scRNA-seq, scATAC-seq, CITE-seq, multiome assays, trajectory inference, cell-state annotation, and cross-sample integration.

Lecture 9-10 introduce spatial genomics, tissue architecture, deconvolution, cell–cell communication, spatial niches, and integration with histology.

Readings/Bibliography

Students will be provided with slides and scientific articles from the recent literature.

Teaching methods

lecture slide PowerPoint presentations


Reading and critical analyses of scientific articles

Assessment methods

The examination procedures will be discussed with the students at the beginning of 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.

With regard to the assessment of learning, limited, declared, and non-substantial use of AI is permitted for support activities, such as summarising and rephrasing. Substantial use of AI to complete any part of the assessment is not allowed..

Teaching tools

powerpoint slides and scientific articles

Office hours

See the website of Giovanni Perini

See the website of Nicola Facchinello