99475 - Eukaryotic Genomes

Learning outcomes

At the end of the module the student has knowledge of the main NGS techniques applied to the sequencing of eukaryotic genomes and to the functional analysis of genomic regions. The successful student has an in-depth understanding of genome assembly and annotation, gene organization, genomic regions and of eukaryotic genome anatomy. In addition, the student is able to frame the biotechnological breakthroughs applying to the structural and functional analysis of eukaryotic genomes, transcriptomes and interactomes in order to explore and predict the functional correlation between gene interaction and phenotypic traits.

Course contents

Eukaryotic genome organization

Sequencing and annotation of genomes. NGS technology.

Genome size, genes and replication origins. Gene organization and gene activity in eukaryotes: gene ontology. Repetitive sequences: families, structures and functions. Organization of mitochondrial and chloroplast genomes. Genome variations: polymorphisms. DNA methylation, CpG dinucleotide and transcription. 

Structural organization of chromatin. Nucleosome: histones and X-ray structure. Post-translational modifications of histones. Translational and rotational positions of nucleosomes.

Expression of eukaryotic genomes

Pervasive transcription of genomes and transcripts classes. Eukaryotic RNA polymerases. Structure of RNA polymerase II. Promoter classification and organization. General transcription factors and their functions. Mechanisms of initiation, elongation and termination of transcription.

Transcription regulation. Upstream and inducible transcription factors. Enhancers. Protein domains of DNA binding: structure and functions. Chromatin regulation of transcription. Genomic maps of transcription factor-binding sites.

mRNA maturation. 5'-end capping and 3'-end maturation. Intron classification: mechanisms of intron splicing.

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/for-students ) 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.

 

Readings/Bibliography

Weaver RF. Molecular Biology.  McGraw-Hill. Last edition.

Capranico et al. Biologia molecolare, Edises 2° Edition (Italian).

Teaching methods

Lectures in english with multimedia presentations. Selftests during the course. Exercises with the UCSC Genome browser.

Assessment methods

Written and oral exam. 

The exam will determine the level of knowledge of the student of the topics discussed during the lectures and the analytic procedures of genomes in UCSC Genome browser.

The minimum score to pass the exam is 18 out of 30.

Teaching tools

Lecture presentations, articles and any other teaching material will be made available immediately to all students.

Links to further information

https://site.unibo.it/capranico-lab/en

Office hours

See the website of Giovanni Capranico