Structure and expression of eukaryotic genomes

Teachers: 
Credits: 
9
Site: 
PARMA
Year of erogation: 
2021/2022
Unit Coordinator: 
Disciplinary Sector: 
MOLECULAR BIOLOGY
Semester: 
Second semester
Year of study: 
1
Language of instruction: 

Italian

Learning outcomes of the course unit

Acquiring knowledge and understanding.
The objective is for the students to gain solid and thorough knowledge of the organization of genomes and on the mechanisms and regulation of gene expression in eukaryotic organisms, with emphasis on the emerging roles of noncoding RNA (ncRNA) in gene regulation.

Applying knowledge and understanding.
Through guided analysis of key experiments for the molecular understanding of some aspects of eukaryotic gene regulation, the students are expected to strengthen their competence in addressing the experimental study of novel gene expression regulatory pathways and of the involved molecular mechanisms, and the identification and characterization of novel regulatory ncRNAs.

Prerequisites

Good knowledge of the structure of nucleic acids and the basic mechanisms of duplications, transcription, repair and recombination of DNA.

Course contents summary

Eukaryotic Genomes: Unique sequences, repeated sequences and informative content of eukaryotic genomes; fraction of genes expressed in a single cell type. Molecular anatomy of a eukaryotic gene: conservation of exons nd their structural organization and high intronic variability; evolution of genomes and possible functional significance. Tandem repetition of rRNA genes. Highly repeated sequences and satellite DNA: evolution of satellite DNA mediated by unequal crossing-over events; minisatellites and genetic mapping. Retrovirus, retrotransposons and interspersed repeated sequences; structure, life cycle and mobilization of retroviruses; retrotransposons, SINE and LINE sequences and processed pseudogenes. Organellar genomes: circular DNA molecules of mitochondrial and chloroplast genomes. Mapping of genomes.
Chromatin and transcription: Chromatin, chromosomes and gene activation: the problem of genomic compaction; the nucleosome as the fundamental subunit of chromatin; organization and assembly of octameric histones; phasing nucleosomes, hypersensitive sites; histone covalent modifications; higher order structure of chromatin;
centromeres, telomeres and structure of chromosomes. Eukaryotic transcription. Eukaryotic RNA polymerases; eukaryotic promoters; transcription machineries of RNA polymerases I and Ill; RNA polymerase II transcription apparatus; eukaryotic transcription control mechanisms; regulatory "in cis" sequences; regulatory trans­acting factors; DNA binding and transcriptional activation; structural protein motifs involved in DNA binding and transcriptional activation. Transcription regulation mechanisms through "enhancers", "silencers" and "insulators"; chromatin structure and its effects on transcription; histone code; structural and functional organization of euchromatin and heterochromatin; covalent and non-covalent modifiers of chromatin; genomic imprinting.
Regulatory RNAs: siRNA and RNAi, miRNA, ncRNA and gene regulation. Long noncoding RNAs. Maturation of RNA. Adjustment of RNA processing mechanisms. Alternative splicing; editing of primary transcripts. Coordination of RNA processing events. mRNA stability control systems.
Eukaryotic translation: mechanism and regulation.
Mechanisms of supramolecular gene regulation: nuclear and cytoplasmic organization mediated by "phase transitions".

Recommended readings

Reference textbooks
LODISH et al., MOLECULAR CELL BIOLOGY, 8th edition, W.H. Freeman & C. publishers, 2016;
also available in Italian translation (less updated edition):
LODISH et al., BIOLOGIA MOLECOLARE DELLA CELLULA, Zanichelli (2009), 3rd italian edition on the original edition.
Other textbooks
WATSON D. et al. - BIOLOGIA MOLECOLARE DEL GENE, settima edizione, Zanichelli 2015
AMALDI et al. – BIOLOGIA MOLECOLARE, seconda edizione, CEA 2014
CRAIG N. et al. – BIOLOGIA MOLECOLARE-Principi di funzionamento del genoma. Pearson 2013.

Teaching methods

The course consists of lectures on key topics in the program, and in-depth focus on topics of particular relevance and interest, with the use of original scientific articles and the assistance of specialist researchers.

Assessment methods and criteria

Evaluation of the expected achievements will be based on an oral interview/test. The test is devised to evaluate both the molecular-level knowledge of gene expression and regulation mechanisms illustrated during the course, and the ability to apply such a knowledge to addressing and solving experimental problems.
The test is devised to evaluate both the molecular-level knowledge of gene expression and regulation mechanisms illustrated during the course, and the ability to apply such a knowledge to addressing and solving experimental problems.