STRUCTURAL AND FUNCTIONAL GENOMICS

Students deepen the knowledges on the organization of the genome into the metaphase chromosomes and interphase nuclei, also considering the evolutionary aspect. They will understand the correlation between architecture of chromatin, gene expression and the onset of human genetic diseases. From the application point of view, the students will acquire the methodological skills on the analysis of human chromosomes and of genomic sequences that can be used in various fields of work, publics and privates.

Lectures and exercises in the classroom with ongoing tests.

The eukaryotic genome. Overview of sizes, the gene content and organization of the sequences in the nuclear genome and in the genomes of cytoplasmic organelles. General aspects on the evolution of the eukaryotic genome. The origin of genomes. Formation mechanisms of new genes.

Methods for chromosome study. The in vitro cultures of cells. Standard techniques for the preparation of metaphase and prometaphase chromosomes. The chromosomal banding: structural and dynamic banding. The International System for Cytogenetic Nomenclature (ISCN). The identification of human chromosomes with G-banding. The fluorescence in situ hybridization: general principles, probe labeling methods and signal detection. The hybridization on chromosomes, nuclei and chromatin fibers. Classical and molecular cytogenetics in biomedical diagnostics. The study of the genomes at the chromosomal level in the post-genomic era. The karyotypes of the Vertebrates and the microchromosomes of Birds and Reptiles.

Structural organization of the eukaryotic genome. Centromeres, telomeres and replication origins. The highly and moderately repetitive sequences. The L1 and Alu sequences. The highly polymorphic sequences and their use in standard protocols for genetic analysis in the forensic field. The gene families. The organization of the genes in the chromosomes.

Compositional organization of the eukaryotic genome. The CsCl gradient for the study of genomes. The main band and the satellite DNA. Compositional features of the cold-blooded and warm-blooded vertebrate genome. The isochore organization of the genomes and the Bernardi model. Structural and functional features related to the isochores. Models of evolution of the vertebrate genome. The "majors compositional shift" and the "minor compositional shift". The newgenome and the paleogenome. Hypotheses on the origin of the GC-rich isochores. The compositional organization of the plant genome.

Functional organization of the chromatin in the interphase nuclei. Th einterphase chromosomes: chromosome territories and interchromosome domain. The Cremer model. Speckles and their organization. Correlation between gene distribution, chromatin structure and gene expression. The constitutive genes and the tissue-specific genes: compositional and structural characteristics and chromosomal distribution. The expression level of the chromosomal bands. Position-effect and the ectopic activation of genes. Features of transcriptionally active and transcriptionally inactive chromatin. The post-translational modifications of histones. DNA methylation and genomic imprinting. LCR and ICR: features and gene activation/inactivation modes. Uniparental disomy syndromes and the genetic diseases related to imprinting. The heterochromatin and the gene inactivation mechanism. Analysis of the organization of the nuclear DNA by means of chromatin conformation capture (3C, 4C, 5C, Hi-C).The inactivation of the X chromosome and the Xist gene.

The educational material is provided by pdf file, uploaded to the Studium platform. Also on the Studium platform, scientific articles are provided both in Italian and in English on topics related to the program.