Genomics and regulation of gene expression

Degree course: 
Corso di Second cycle degree in MOLECULAR AND INDUSTRIAL BIOTECHNOLOGY
Academyc year when starting the degree: 
2016/2017
Year: 
1
Academyc year when helding the course: 
2016/2017
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

SUBJECT GOALS
Introduction and training goals
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 course’s training goals are a detailed knowledge of genomic sciences and both the experimental approaches and main achievements in the field of genomics, a deep comprehension of the main mechanisms underlying en expression regulation eucaryotes and the ability to carry out bioinformatics analyses on the currently used genome browsers.

LEARNING OUTCOMES
Knowledge and understanding (Knowledge and know)
Achievement of 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. Development of a critic awareness and ability to analyze and discuss issues related to the course contents.
Applying knowledge and understanding (Skills and know how)
Achievement of the ability to apply the acquired knowledge, at both theoretical and practical levels, in relation to the professional approach. Achievement of the comprehension skills required to develop and maintain issues related to the acquired knowledge, by means of critical reasoning and problem-solving attitudes. Achievement of the ability to solve a wide range of problems and issues related to the course contents with the aid of bioinformatic tools.

GENOMICS CLASS (4 CFUs, 32 hours)
• Course introduction: theoretical bases of Genomics.
• Genome project, part 1: Rationale, aims and planning. Human genetic maps. Linkage analysis and autozygosity mapping in humans.
• Genome project, part 2: physical maps of the human genome: somatic cell, radiation hybrids and clone contig maps. Transcriptional maps (EST project).
• Genome project, part 3: Public and private human genome sequencing approaches and validation of the sequence assembly.
• Post-genomics Genome annotation. GeneOntology and EnCODE projects.
• Functional Genomics: Forward and reverse genomics.
• Genetic dissection of complex diseases: Linkage disequilibrium mapping. SNP markers and the HapMAp project. Genome-wide association studies. Introduction to personal genomics. The 1000 genome project. .Mapping disease genes by exome sequencing.

REGULATION OF GENE EXPRESSION CLASS (1 CFU, 8 hours)
• Gene expression in procaryotes and eucaryotes.
• Chromatin structure, chromosome territories and transcription factories.
• Epigenetic modifications and gene expression. The histone code.
• Cis-acting regulatory elements: promoters, enhancers, silencers and insulators.
• Post-transcriptional regulation
• Genomic imprinting

LABORATORY MODULE (1 CFU, 16 hours)

The Laboratory section is organized in four lessons focused on the use of bioinformatics tools for the resolution of problems in the field of genome sciences by means of several free-access bioinformatic programs and databases.

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:
• TA Brown – “Genomes 3” (Garland Science Publ.)
• T Strachan & A. Read – “Human Molecular Genetics” (Garland Science Publ.)
• J Watson, R Meyers, A Caudy & J Witkowski - “Recombinant DNA: genes and genomes” (W.H. Freeman & Co)

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.

Professors