Learning objectives
The aim is to provide an in-depth knowledge on the mechanisms
controlling eukaryotic gene expression at both the transcriptional and
post-transcriptional level, taking into account the information recently
made available by genomics. This will be pursued through a unifying
conceptual framework pointing to general regulatory strategies shared by
prokaryotes and eukaryotes and by different phases of the genetic
information transfer process (transcription, mRNA splicing and other posttranscriptional
events, controlled modification/degradation and
subcellular localization of proteins, signal transduction to the cell
nucleus). Both theoretical and practical aspects of gene expression
control will be considered, with special emphasis on its biomedical and
molecular diagnostics applications/implications.
Prerequisites
Basic knowledge in chemistry, biochemistry, molecular biology and
genetics.
Course unit content
Structure of eukaryotic genomes.
Regulatory strategies relying upon “regulated recruitment”.
Eukaryotic RNA polymerases, transcriptional regulators and promoters.
Chromatin and nucleosomes.
Enhancers and different modes of control of eukaryotic transcriptional
regulators.
Other cellular processes relying on “regulated recruitment”.
Full programme
Structure of eukaryotic genomes: repeated sequences and gene
duplication, (retro)transposable elements, simple and complex
transcription units, multigene families, regulatory sequences and
differential gene expression.
Regulatory strategies relying upon “regulated recruitment” (key
examples from prokaryotic systems); activator bypass experiments and
the “two-hybrid” technology; “squelching” and transcription factor
decoys; regulated recruitment and cooperativity; other types of gene
regulation processes (RNA polymerase modification; DNA modification).
Eukaryotic RNA polymerases, transcriptional regulators and promoters.
General transcription factors (GTFs); pre-initiation complex formation;
“mediator”; (co)activators and (co)repressors; the Saccharomyces
cerevisiae activator Gal4; the negative regulators Gal80 and Mig1; the
other eukaryotic transcription systems (RNA pol I and RNA pol III); postinitiation
events (capping, splicing and polyadenylation); the
“spliceosome, splicing regulator elements (ESE, ESS and ISS) and splicing
regulation.
Chromatin and nucleosomes; chromatin remodeling and histone
modification (HAT, HDAC, HMT, HDMT); regulatory roles of histone tail
modification (acetylation/deacetylation; methylation/demethylation);
chromatin immunoprecipitation (ChIP); combinatorial control: mating
type regulation in Saccharomyces cerevisiae; telomeres and their
associated regulatory effects; DNA methylation; insulator sequences and
other higher-order control elements.
Enhancers; different modes of control of transcriptional regulators;
nuclear receptors; SREBP; Tubby; Notch and APP; NF-kB, TAT/TAR, Rb and
cyclins.
Other cellular processes relying on “regulated recruitment”:
ubiquitination and controlled degradation of selected target proteins,
hormone-receptor interaction and signal transduction pathways directed
to the nucleus.
Bibliography
Lodish H., Kaiser C.A., Bretscher A., Amon A., Berk A., Krieger M., Ploegh
H., Scott M.P.
MOLECULAR BIOLOGY OF THE CELL (Seventh Edition)
Macmillan Higher Education/Freeman and Company Publishers
Watson J.D., Backer T.A., Bell S. P., Gann A., Levine M., Losick R.
BIOLOGIA MOLECOLARE DEL GENE/MOLECULAR BIOLOGY OF THE GENE
(Sixth Edition)
Zanichelli/CSHL Press; Pearson/Benjamin Cummings Publishers
Ptashne M., Gann A. "GENES AND SIGNALS", Ed. Zanichelli
Reviews, selected articles and powerpoint presentations from companies
in the field of Chemogenomics, which will be made available to the
students in an electronic format.
Teaching methods
The course is mainly based on lectures, but also includes exercises, the
examination/discussion of original scientific articles and examples of data
analysis.
Assessment methods and criteria
Evaluation of the expected learning achievements will be based on an
oral examination that will also include the discussion of specific
regulatory schemes, application examples/case-studies and discovery
strategies presented in the course. This will allow a detailed evaluation of
the theoretical and practical knowledge on the various genetic
information transfer/elaboration processes illustrated in the course as
well as the ability to apply such knowledge to address and solve specific
experimental problems.
Other information
Students are expected to acquire a detailed knowledge of some of the
most important cellular and molecular processes underlying the
elaboration of eukaryotic genome information and related applications,
especially with regard to bio/molecular medicine. Special emphasis will be placed on post-genomic experimental strategies that are being
employed to discover and/or functionally characterize novel bio-active
compounds.
APPLYING KNOWLEDGE AND UNDERSTANDING.
Through the guided analysis of key experiments that have allowed to
understand some of the above described processes, students will acquire
the basic knowledge and competence required for the study of genetic
information transfer/elaboration processes at the molecular level and for
the exploitation of genomics as a tool for the functional characterization
of bio-active small-molecules and the identification of novel compounds.
