67167 - Functional Genomics with lab

Learning outcomes

Students will know the organization of eukaryotic and prokaryotic genomes, and the gene expression regulation. The students will receive basic and advanced knowledge on the microarray methodologies and their applications, on the high throughput nucleic acids sequencing technologies, and the organization of major public genomic databases. Moreover, students will know advanced aspects of transcription regulation at a global level and will know how to retrive and analyze data from genomic- and  post-genomic databases.

Course contents

The course is organised in two modules:

1) Eukaryotic Functional Genomics: modern definition of the genome, different ways in which gene expression can be regulated, epigenetic modifications. Basic research with DNA microarrays. Introduction to microarrays. Microarrays Experimental Design: target genes to spot, RNAs source, replicates, hybridization, analysis and normalization. Statistical analysis of microarrays data: fluorescence signal analysis, background levels, lowess methods and M/A plot. High-throughput nucleic acids parallel sequencing technologies. Major and more recent sequencing platforms. Application of sequencing technologies to the reconstruction of the eukaryotic genome, to the reconstruction and analysis of the transcriptome, for mapping interactions between genomic DNA and proteins, for mapping interactions between RNAs and proteins, for the identification of epigenetic modifications (e.g. cytosine methylation), for the identification of regulativeinteractions between genomic loci.

2) Prokaryotic Functional Genomics: Molecular mechanisms governing gene expression in prokaryotes: an overview. Characterization of bacterial transcriptome through RNA-sequencing (genome annotation e differential gene expression analysis). Differential RNA-sequencing: a novel genome-wide approach to map transcription start sites. Dual RNA-sequencing for the study of host-pathogen interaction: a novel approach to simultaneously analyze changes in gene expression occurring in both the pathogen and the host. Selective immunoprecipitation of double stranded RNA formed in vivo to study antisense RNA regulation. Combination of RNA-seq and ChIP-seq to dissect complex transcriptional regulatory networks. Characterization of the process of translation through Ribosome Profiling.

Laboratory: The practical part of the course will consist of exercises on the use of the UCSC genome browser to lear how to access and analyze the stored data, and on the use of the web-server Galaxy for the analysis of transcriptome sequencing data.

Readings/Bibliography

Articles and reviews indicated by the teacher.

Teaching methods

Lectures and PC work assignments. Practical use of UCSC genome browser and of Galaxy for accessing and analyzing genomic data.

Assessment methods

The exam will assess if the student knows the organization of eukaryotic and prokaryotic genomes, and how to analyze gene expression and its regulation. The exam will also assess if the student knows how to access UCSC Genome database, and how to retrieve and analyze genomic data using the UCSC genome browser and Galaxy.

The exam will consist of: a) an evaluation test of the methodologies described in the laboratory; b) a written exam on the course arguments, and c) an optional oral exam.
The maximum score will be 30/30.

Teaching tools

PC, internet, videoprojector, board.

Bioinformatic laboratory at the Biotecnology Education Center at "Navile".

Office hours

See the website of Fabrizio Ferrè