Gene Regulation

Course manual 2025/2026

Course content

To function optimally as a eukaryotic organism, genes must be selectively expressed at the right time and tissue, and transposons must be inactivated. This complex process involves a wide range of molecules, genetic and epigenetic mechanisms, for example regulatory elements, transcription factors, histone and DNA modifications, non-coding RNAs, and chromatin folding. The mechanisms underlying gene regulation are mostly evolutionary conserved, from yeast to plant to human. In this course, knowledge obtained from all these organisms will be discussed with the students in an integrated way. The lectures contain a lot of material from very recent literature.

The following topics are covered:

• Modern technologies used in gene regulation research
• Transcription factors
• Cis-regulatory elements
• epigenetics
• 3D genome organization
• histone modifications
• histone variants
• Chromatin remodeling
• DNA methylation
• Polycomb silencing
• non-coding RNAs (siRNAs, piRNAs, miRNAs, long non-coding RNAs)
• epigenome editing

Study materials

Literature

• Molecular Biology of the Cell (7th edition) by Alberts et al. 

  Epigenetics by David Allis et al (ISBN  978-1-936113-59-0) is very useful, but not mandatory.

Other

• Slides of the lectures, notes made by students and other material provided

Objectives

• The student can discuss various gene regulation mechanisms.
• The student can discuss the effects of genetic and epigenetic modifications on the development of an organism.
• The student can explain different techniques for RNA, DNA and chromatin analysis.
• The student can transfer knowledge gained about gene regulation from lectures and literature orally to fellow students.
• The student can critically analyze scientific publications in the field of gene regulation.
• The student develops one's own opinion about science and scientific results.
• The student can discuss current issues of gene regulation.
• The student can, together with other students, apply the obtained knowledge to design a Project

Teaching methods

• Lecture
• Computer lab session/practical training
• Self-study
• Presentation/symposium
• Working independently on e.g. a project or thesis
• Supervision/feedback meeting

Education is given in the form of lectures, a practical and a number of assignments in which, among other things, recent publications are analyzed, but also in which acquired knowledge is translated into the design of a project. The computer practical and assignments contribute to broadening and deepening of the knowledge of the material taught in the course. The practical and assignments are carried out in small groups (2-3 students).

During the computer practical, DNA methylation data analysis is performed on data that will be provided by the teachers. The other assignments consist of presenting and discussing scientific articles and devising an experimental approach to find the answer to a specific scientific problem (Project Design).

The hours stated below do not include the required self-study. For each Journal club we expect students to have about 5 hours of self-study, for the design project we anticipate 10-12 hours of self-study.

Learning activities

Attendance

Additional requirements for this course:

• Participation in all practical sessions, tutorials, Journal clubs and Project Design sessions is obligatory. In case one cannot attend for valid reasons this has to be communicated to the course coordinator before the activity takes place.
• Attending all lectures is highly recommended; the lectures also contain recently obtained knowledge that is best understood when students attend the lectures (and make notes).
• For the Journal Clubs and Project Design students have to work together in small groups; absence of group members negatively influences the final mark for a group and is undesirable.
• In case a student is absent for the Journal club or Project Design sessions the student will get an alternative  assignment.

Assessment

- The final grade is determined on the basis of the grades for the components.

- The student has passed the course if the final grade is at least 5.5 and if the exam has been scored at least 5.

- Journal Club: 15% of the final grade

- Practical: 15% of the final grade

- Project Design: 15% of the final grade

Inspection of assessed work

The grades of the assignments and practical and the exam will be provided and explained through canvas.

For the exam one separate meeting will be arranged at which students can see their own answers. At this meeting the answer models will be explained.

Assignments

Journal Club

For the Journal club assignment (twice), students must analyze provided articles on gene regulation. For both Journal Club meetings student groups of two are assigned one of the Figures in the paper that they need to present (in a slide) and discuss. When presenting, other students in the group should ask questions to the students presenting (students have to prepare questions upfront). This assignment is assessed (15% of final grade) using an assessment form.

Practical

The students learn interpreting the obtained data and translating the results to the questions asked. This assignment is performed in groups of 2 students and is assessed (15% of final grade)

Project Design

Students must apply the knowledge acquired in the course to think about the experiments to be done, in what order, to get an answer to the given scientific problem. There is one feedback moment on the ideas of the students at the start of week 3. At the start of week 4 the students present and defend their approach to fellow students and the lecturer. This assignment is done in groups of 3 students and assessed by the lecturer of the group (15% of final grade).

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

Processed student feedback

Compared with last year:

• The tutorials are more spread out over the course
• The experimental part of the practical is taken out; now the practical is only focused on data analysis
• The main lecturers will mark the slides that are important for the exam (for example by a star)
• The number of Questions at the exam will be decreased

Contact information

Coordinator

• dr. M.E. Stam

Staff

• dr. R.A.F. Gjaltema
• Ing M. Bliek
• prof. dr. V.M. Christoffels
• dr. E. de Wit
• prof. dr. ir. R.C. Schuurink
• dr. G. Dugar
• dr. T. van Boxtel
• K. Peek MSc
• dr. J Breil-Aubert
• Reza Shogi MSc