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Academic year 2017/2018

Course ID
Teaching staff
Prof. Michele De Bortoli
Prof. Santina CUTRUPI
Degree course
Cellular and Molecular Biology
1st year
Teaching period
Second semester
Course disciplinary sector (SSD)
BIO/11 - biologia molecolare
Formal authority
Lessons optional and laboratories mandatory
Type of examination
Written and oral
No specific prerequisite is indicated in addition to the Syllabus for Master course admission. Nevertheless, for a full comprehension of the subjects of this course Students must be familiar with basic Molecular and Cellular Biology and basic Genetics and Bioinformatics.

Sommario del corso


Course objectives

Students will acquire an advanced level of knowledge on the activity of genes and genomes and the mechanisms of genome regulation at the transcriptional and post-transcriptional level, in the contexts of development, differentiation, cellular homeostasis and cancer.

In the first part of the course Students will understand how the modern global methods (microarrays, Next Generation Sequencing, epigenomics, protein-DNA, protein-RNA, proteomics), make it possible to represent the organization and control of most evolved genomes.

In the second part of the course, Students will acquire the ability to use their theoretical knowledge in solving applicative problems, with special regard to biomedical issues, through the study of literature. In particular, Students will learn how to associate the genomic variants with possible control functions and with disease states.

Specific objectives are to:

  1. make the point on the evolution of Molecular Biology since the completion of the Human Genome Project and the advent of high throughput genome sequencing technologies
  2. discuss the advancements in regulatory Biology produced by Genomics, with specific regard on the regulation of gene expression and gene interaction at the network level
  3. introduce students to the understanding of molecular biology at the systems level
  4. guide students to the reading and interpretation of research articles in the field of regulatory molecular biology
  5. allow students to perceive what applications the new genomics studies can generate, particularly in the fields of medicine and neurobiology.

Results of learning outcomes

Expected outcomes, divided in “knowledge, understanding, abilities”, are:


  • the most common analytical methods in Genomics and transcriptomics, comprising the fundamentals of bioinformatics analysis of results
  • the most important modalities of transcriptional regulation in higher Eukaryotes.
  • the mechanisms of alternative RNA transcript generation, including non-coding RNAs and associated functions.
  • the constitutive principles of gene regulatory networks
  • the involvement and the changes of components of those networks in human disease


  • how a molecular biology study, aiming at a knowledge of the above, is planned and conducted; how results are presented and discussed in a primary scientific journal; and finally how results must be understood and analyzed in the framework of current knowledge.
  • what kind of methodological approach (among those studied) should be used to answer a specific scientific question.
  • what information can be obtained from genomic analysis to understand the molecular mechanisms associated with diseases;
  • how to use this knowledge to develop a potential therapeutic strategy


  • to do literature searches on the course topics
  • to search for information on and expose a summary of the main methods of genomics and functional genomics
  • to analyze, interpret and report publicly on a recent scientific article, including the methodology used, concerning one of the course topics
  • to interpret results and diagrams relating to the main issues discussed
  • to expose briefly one of the topics of the program, with specific reference to genomics and methodology
  • to individuate which methods should be used to address a specific problem in the field



Course delivery

The first part of this course is composed of 5 Chapters, with a total of 40 hours lecturing, plus Moodle’s support activities, hands-on bioinformatics laboratory and Students’ Report activity, corresponding to 6 cfu. The second part is composed of 20 hours lecturing, reading and discussion of scientific results, corresponding to 3 cfu.



Learning assessment methods

The ability to search, analyse and report results of recent scientific papers on the course subjects is achieved through a practical “Students’ report” activity. It is evaluated as such, together with an evaluation of Student’s participation to e-learning support activities.  1) congruence; 2) difficulty; 3) contextual framework; 4) analysis of results; 5) comprehension; 6) clarity of report, are graded. The level of participation in support activities and bioinformatics hands-on laboratory is evaluated as % participation, quiz or lesson execution, and writing in methodological Wikis. Grading is out of 30, with “cum laude” counted as 33/30.

The ability to interpret experimental results and schemes is evaluated by a Moodle-based test, which is composed of 15 questions in which, based on Figures extracted from scientific papers or reviews discussed during course lectures, Students are required to answer questions (multiple choice, short answer, short essay). Grading is out of 30, with “cum laude” counted as 33/30.

The ability to expose and discuss course topics is evaluated through a short interview, usually no longer than 30 minutes. During first 10 min Students are expected to expose a general topic at Teacher’s choice among a list published in advance on the course website. There will be no break and no question in this first period. A specific question may be offered at the end. Finally, during last 10 minutes, a Figure from one of the 5 Research Papers discussed during the course is chosen and Students are required to explain in detail the experiment.  Grading is out of 30, with “cum laude” counted as 33/30.

The final grade is the mean of the three single grades. The “cum laude” is assigned when one of the single grades is “cum laude” (33/30) and the general average is above 30. 


Support activities

Support activities are organized on the Moodle e-learning platform ( ). Activities such as quizzes, lessons, and guided website visualization are posted and participation monitored. Two students’ wikis are organized, one for the search of Research papers for Students’ Report and one concerning methodological aspects. Last, for each chapter of the course, Research papers are posted that Students must read and that are discussed thoroughly during the lessons.



  1. Nuclear topographic organization, chromosomal territories, eu- and hetero-chromatin and functional aspects.
  2. Genomics and post-genomics, NGS technologies, epigenomics, genomic imprinting, chromatin dynamics and functional domain programming. ENCODE.
  3. Transcriptomics, microarray and RNA-seq technologies. Genic Unit and transcript variants. Non-coding RNAs. Genomic databases.
  4. The regulation of gene transcription. Promoters, CpG methylation, nuclear positioning. Coregulators, Transcription Factors, enhancers, signal transduction. LncRNA role in transcriptional regulation and chromatin dynamics.
  5. Alternative splicing: regulatory factors and mechanisms. Stability, decay and intracellular localization of RNAs. RNA interference. MicroRNA, lncRNAs and transcriptional and post-transcriptional regulatory circuits.
  6. The role of transcriptional enhancers in cell identity definition, in tumor progression and in other diseases.
  7. Super-enhacers: characterization and functional aspects in human diseases
  8. Epigenomics of Alzheimer Disease and Multiple Sclerosis.

Suggested readings and bibliography


There is no specific textbook for this course. For basic and general reference, recent (>2010) editions of any Molecular Biology textbook for undergraduate students will be OK.

As a support for the study of this course, specific scientific Reviews are posted on the Moodle course website. Websites containing support videos, texts, images and other materials are also indicated.


Class schedule

Notes: See the timetable at the Class Schedule Page

Last update: 21/06/2017 11:15
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