Ateneo - UPO

After a quick review of gene structure in eukaryotes and prokaryotes, the issue of gene expression regulation will be presented.
The first part of the course will deal with prokaryotes gene expression and its regulation. A series of examples will illustrate the possibility of engineering promoters and genes for biotechnological purposes.
The second part of the course will deal with the eukaryotes gene expression and the multiple levels of its regulation. Issues: 1) chromatin organization and structure, 2) transcription factor function, 3) pre-initiation complex, 4) transcription termination, 5) RNA stability and 6) RNA translation.
The third part of the course will deal with the mechanisms by which extracellular signals and intracellular cues regulates gene expression in eukaryotes. A particular emphasis will be placed on the alterations of gene expression in cancer and on the regulation of gene expression in function of nutrients and metabolic status of the cell.
Basic molecular biochemical and biological techniques will also be presented.

For the improvement of students background
- Harper's Illustrated Biochemistry, 29e, Robert K. Murray, David A. Bender, Kathleen M. Botham, Peter J. Kennelly, Victor W. Rodwell, P. Anthony Weil
Please note: available on Access Medicine for our students
- Molecular Biology of the Cell - Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter Edition:5th
Please note: the 4th edition is available for free on NCBI bookshelf http://www.ncbi.nlm.nih.gov/books/NBK21054/

Suggested textbook
- Genomes 3 By Terence A. Brown
Please note: the 2nd edition is available for free on NCBI bookshelf http://www.ncbi.nlm.nih.gov/books/NBK21128/
- Cell Signalling Biology Professor Sir Michael Berridge http://www.biochemj.org/csb/
- An extended series of reviews as evidenced during the course.

Enhance knowledge and operational skills in molecular biology applied to the study of gene expression.
Provide the cognitive tools for the critical reading of literature.
Provide the operational bases in the molecular biological laboratory.

Basic Biology: Prokaryotes and Eukaryotes intracellular organization.
Basic biochemistry: DNA and RNA structure and metabolism, protein synthesis, enzyme proprieties, major metabolic pathways.
Basic molecular biology: concept of gene, gene expression, promoter, transcription factor, RNA synthesis and degradation.
For the students lacking a strong background in life sciences a series of readings will be proposed to improve their skills on those topics.

During the course, slides and webinars will be extensively used.
Classwork will be complemented by an introduction in the laboratory.
Students will also undertake teacher driven research/presentation/teamwork.

A copy of the slides and the websites used during the course will be available on the DIR site.

The exam will be written with multiple choice questions (24, worth one point each, divided in 11 "Genomic analysis", 11 "Regulation of gene expression" and 2 "Genetics") and open questions (3, worth 3 points each).

Topic 1
Regulation of gene expression.
Recall of the organization of genes in eukaryotes (enhancers, promoters, transcription initiation site, introns / exons, transcription termination sites). Control of gene transcription at the level of: a) transcription initiation rate, 2) alternative splicing and splicing, 3) mRNA stability, 4) interference between RNA and microRNA. Organization of transcription factors: structure of DNA binding and transactivation domains. Main DNA regulatory sequences. Assembly of the RNApolII transcription initiation complex and hints for other polymerases. Methods for studying the regulatory elements on DNA, the structure of the promoters and the binding sites of transcription factors. Transcription factors and chromatin structure, gene expression and chromatin remodeling. Post transcriptional modifications of histones and the histone code. DNA methylation. Other ways to regulate gene expression: alternative promoters, alternative splicing, mRNA stability control, mRNA translation control, miRNA and RNA interference.

Topic 2 Control of gene expression by extracellular and intracellular signals.
How the signal transduction pathways regulate gene expression: - the nuclear receptor family - the STAT family - ERK signaling for the serum response elements, NF-kB. Methods of studying signal transduction.
Topic 3 mutations in transcription factors and cancer
Mutations of P53 and tumorigenesis, Hif formation in response to hypoxia, myc and tumor amplification.

Case studies: 1) transcription factors and tumor metabolism, 2) how alterations in metabolism (ie habits or cellular energy status) influence gene expression and chromatin status.

Short simulated or face-to-face laboratory experiences on basic techniques.

Understanding of the mechanisms of regulation of gene expression.
Operational use of this knowledge for the evaluation of the literature.
Guided design of experimental paths that can be used for theoretical or applicative research.