Genomics and regulation of gene expression

Degree course: 
Corso di Second cycle degree in MOLECULAR AND INDUSTRIAL BIOTECHNOLOGY
Academyc year when starting the degree: 
2017/2018
Year: 
1
Academyc year when helding the course: 
2017/2018
Course type: 
Compulsory subjects, characteristic of the class
Credits: 
6
Period: 
First Semester
Standard lectures hours: 
56
Detail of lecture’s hours: 
Lesson (40 hours), Laboratory (16 hours)
Requirements: 

A detailed knowledge of Genetics, Molecular Biology and Recombinant DNA Technologies is required. Moreover, a solid experience with the World Wide Web and a basic background in Bioinformatics are strongly recommended. A good knowledge of English will be important to read and understand texts and publications that will be provided to the students as teaching material.

Final Examination: 
Orale

Students will undergo an oral examination. During the exam, the acquired knowledge will be evaluated by raising at least three question focussed on different issues. Questions aimed at evaluating the problem-solving ability of the student will also be posed. A specific question over the laboratory module will also be asked. For each student, the final judgement will consider the quality and precision of the answers (70%), the ability to motivate statements (20%) and the communication skills (10%). The time for the exam is about 20-25 minutes and the exam will be considered passed equal or over the 18/30 mark.

Assessment: 
Voto Finale

This course is organized in two distinct modules, represented by class lessons and a laboratory training section. The course is mainly focused on the recently developed genomic sciences but will also include a section dedicated to the main mechanisms of gene expression regulation. The laboratory section will be focused on the use of several online platforms mostly used in bioinformatics approaches to genomics.
The expected learning outcomes for this course will be the following:
-A detailed knowledge of the principles of genomic sciences and both the experimental approaches and main achievements in the field of genomics, and a deep comprehension of the main mechanisms underlying gene expression regulation eucaryotes.
-The ability to carry out bioinformatics analyses on the currently used genome browsers, in order to elaborate genomic experimental plans as well.
-The ability to carry out bibliography searches and to synthesize the retrieved informations in oral and/or visual representation
- The ability to achieve an informed judgment, adequate expertise and communication skills in relation to both the experimental approaches and main scientific achievements in genome sciences and the mechanisms underlying the regulation of gene expression.
- The ability to develop a critic awareness and ability to analyze and discuss issues related to the course contents and the comprehension skills required to develop and maintain issues related to the acquired knowledge, by means of critical reasoning and problem-solving attitudes

MODULE OF GENOMICS (4 CFUs, 32 hours)
- From Genetics to Genomics: introduction (2 hours)
- Genome project, part 1: Rationale, aims and planning. Polymorphic genetic markers and genetic maps. Theoretical basis of linkage analysis in humans (LOD scores) Autozygosity mapping (6 hours)
- Genome project, part 2: Physical maps of a genome. Somatic cell and radiation hybrids. Physical maps based on FISH assays. Genomic libraries and assembly of clone contigs by fingerprinting or STS-content mapping. Transcription maps of the genome. The EST project (4 hours)
- Genome project, part 3: Human genome sequencing: the “clone-by-clone” e “whole genome shotgun” approaches. The public and private human genome projects. Validation of the human genome sequence assembly (4 hours)
- The post-genomic era: Genome annotation. The informational content of the human genome. Gene number and biological complexity. The GeneOntology and EnCODE projects (5 hours)
- Genome transplantation: an avenue for synthetic life (2 hours)
- Functional Genomics: Forward and reverse genomics approaches (3 hours)
- Genomic approaches for the genetic dissection of complex diseases: Linkage disequilibrium mapping. The advent of SNP markers and the HapMAp project. GWA studies (4 hours)
- Introduction to personal genomics. Approaches for next generation sequencing. The 1000 genome project. .Mapping human disease genes by exome sequencing (2 hours)

MODULE OF REGULATION OF GENE EXPRESSION (1 CFU, 8 hours)
- The molecular bases of gene expression in procaryotes and eucaryotes (1 hour)
- Accessing the genome: nuclear topography and chromatin structure. Chromosome territories and transcription factories (2 hours)
- Epigenetic modifications associated with gene expression. The histone code concept (2 hours)
- Cis-acting regulatory elements: promoters, enhancers, silencers and insulators. Molecular mechanisms of enhancer action. Enhancer prediction by comparative genomics approaches. Locus Control Regions (2 hours)
- Mechanisms of post-transcriptional regulation (0,5 hours)
- Genomic imprinting (0,5 hours)

MODULE OF GENOMICS - LABORATORY (1 CFU, 16 hours)

The Laboratory section is organized in four lessons(4 hours each), with a preliminary introduction followed by training activities carried out in the bioinformatics laboratory. The lab section envisages the use of bioinformatics databases and algorithms for the planning and resolution of a set of topics and problems in the field of genome sciences, mainly by means of the most popular genome browser, such as those hosted at NCBI, UCSC e Ensembl. The lab program will be carried t according to the following schedule:

- Analysis of a human disease pedigree.
- Definition of the map position of candidate disease gene.
- Search for mutations segregating with a human genetic disease.
- Planning the isolation of a the gene toexpress the corresponding gene product.
- Planning of a site-specific mutagenesis assay.
- Bioinformatic search to define the expression levels of a gene of interest and in silico planning of a qPCR assay.
- Search for the putative regulatory regions for a gene of interest by means of in silico analysis of evolutionarily conserved DNA genomic sequences.
- Planning a cloning strategy to express a recombinant fusion protein carrying a FLAG epitope.
- Implementation of a strategy to silence a gene of interest by RNA interference

To carry out the above mentioned tasks, students will make use of several free-access bioinformatic programs and databases, such as Restriction mapper, OFRfinder, NCBI BLAST, Primer3, rVista, TransFac, ClustalW, Oligo calculator, Gene Cards, siRNA Design.

The teaching material is regularly updated and will be provided to all students in the e-learning online platform as Powerpoint slides file, short notes, animation files and articles from scientific literature on selected issues. For the laboratory session, printed folders and extracts from the scientific literature will be provided. All didactic material will be made available to the students through the online e-learning tool.

Recommended textbook:
• T Strachan & A. Read – “Human Molecular Genetics” (Garland Science Publ.)
• T Strachan, J Goodship & P Chinnery – “Genetics and Genomics in Medicine” (Garland Science Publ.)

The course envisions both class lessons (5 CFUs) and laboratory training (1 CFU). Class lessons will be held with the aid of slide presentation sessions, coupled to projection of didactic movies when required. The laboratory training section will be held in the bioinformatics laboratories at the teaching headquarter in via Monte Generoso in Varese. Each student will be given a designated workstation with an online PC( in order to individually carry out the section program) together with a printed folder describing each training section. Assistance to the students will be granted throughout the whole lab sessions. Lab attendance is mandatory for all students, which can skip no more than one lesson for explained reasons.

The teacher will answer questions regarding the topics discussed in the course following an arrangement, either by phone or e-mail. Students are kindly required not to ask bureaucratic/administrative question, if not really urgent. Email address: francesco.acquati@uninsubria.it

Professors