University of Naples Federico II
PhD Program in Molecular Medicine
Molecular biology course on the human genome and its functional elements
Contact Information
Teachers:
Caterina Missero
Office location: CEINGE
Phone: 0813737853
E-mail: missero@ceinge.unina.it
Sandro Banfi
Office location: TIGEM
Phone: 0816132206
E-mail: banfi@tigem.it
Course Information
Semester & year: Fall 2012
Meeting days & time: January 15-18
Meeting location: Biological Tower, 1° floor
Course Description
The main focus of the course will be dedicated to the human genome project and the identification of
the functional elements in the human genome. These topics will cover gene annotation, transcriptome
analysis through ultra-deep identification of coding and non-coding RNA, regulation of transcription at
genome-wide level, and chromatin analysis. The teachers will introduce the ENCODE (ENCyclopedia
Of DNA Elements) project and will describe the experimental approaches as well the way to access to
these data. A tutorial on how to access the ENCODE data in the UCSC Genome Browser will be given.
Original papers on the topics and practical analysis of ENCODE data will be presented by the students.
Background Preparation (Prerequisites)
Students should read relevant background from the suggested textbooks, before classes. Even students
who have not previously taken a Molecular Biology course will be able to successfully take this course
if they read relevant background material from the books. Suggested textbooks are: Watson et al.
Molecular biology of the gene; Lewin, Genes; Weaver, Molecular Biology.
Course Learning Outcomes
By taking this course students will become progressively able to:
1.
analyze papers in the literature;
2.
conduct critical analysis of contemporary basic research in genomics;
3.
discuss essential concepts in transcription regulation in eukaryotes;
4.
demonstrate proficient verbal communication skills that reflect scientific analysis of the
literature;
5.
demonstrate proficient scientific writing skills that reflect scientific analysis of the
6.
literature;
analyze available human genomic data.
Course Requirements & Assignments
At the end of each class, the teacher will distribute papers pertinent to the topic addressed. Students
will prepare a text (in English) in which they: i) briefly describe the main points of the papers; ii)
briefly describe the experiments done and the logic of the experimental design.
In the fourth class students will prepare a functional analysis of a given human genomic region based
on the data available in Genome Browser.
Grading
Student progress will be assessed on the basis of:
1.
evaluation of participation in discussion, 20%
2.
writing assignments
40%
3.
functional analysis of genomic region
40%
Grading of students’ papers will be based on overall clarity, logical presentation, demonstration of
understanding of the subject matter, logic and feasibility of the proposed experimental approach.
Point grades for each category will be: 3 points = excellent (A), 2 points = very good (B), 1 point = fair
(C), 0 points = unsatisfactory (D).
Class format
The course consists of four classes. In classes 1-3 (2 hours each) the topics indicated below will be
presented by the teacher and discussed. After each class the students will received papers to the topic
addressed and will have to prepare a written assignment. At the beginning of each class the previous
topics will be briefly discussed. In the last class students will present their functional analysis of a
human genomic region in a Power Point Presentation.
Schedule
1
Date
January 15
Time
10:00-12:00
2
January 16
10:00-12:00
3
January 17
10:00-12:00
4
January 18
10:00-12:00
Subject
The human genome
sequencing and next
generation sequencing
Transcriptome: coding and
non-coding RNA
Regulatory sequences in the
human genome
Student presentations on
ENCODE data access on
USCS genome browser
Supervisor
Missero
Banfi
Missero
Missero
Selected Bibliography
1) An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium
Nature. 2012 Sep 6;489(7414):57-74.
2) The long-range interaction landscape of gene promoters. Sanyal A, Lajoie BR, Jain G, Dekker J.
Nature. 2012 Sep 6;489(7414):109-13.
3) ENCODE Data in the UCSC Genome Browser: year 5 update. Rosenbloom KR, et al. Nucleic Acids
Res. 2012 Nov 27
4) Architecture of the human regulatory network derived from ENCODE data. Gerstein MB, et al.
Nature. 2012 Sep 6;489(7414):91-100.
5) Landscape of transcription in human cells. Djebali S, et al., Nature. 2012 Sep 6;489(7414):101-8.
6) The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature. 2012 Sep
6;489(7414):75-82.
7) Next-generation genomics: an integrative approach. Hawkins RD, et al. Nat Rev Genet. 2010
Jul;11(7):476-86.
8) Sequencing technologies - the next generation. Metzker ML. Nat Rev Genet. 2010 Jan;11(1):31-46.
WEB sites:
nature.com/encode
http://encodeproject.org