Genomes and Gene Expression


Course Objective

Course objectives:
The student should be able, at the molecular level, to
- describe the composition of eukaryotic and prokaryotic genomes and
identify and indicate the function of the different sequences
- explain and dissect the process of transcription initiation, -
elongation and - termination, and how these processes are regulated,
mainly in eukaryotes
- describe in detail the structure and composition of chromatin, the
post-translational modifications of histone proteins, the enzymatic
machinery involved and their control
- distinguish between general and the various types of specific
transcription factors, and explain their collaboration to induce or
repress gene expression
- describe the various forms of DNA modification, their biochemistry,
and impact on genome maintenance and gene expression in various somatic
- describe the epigenetic reprogramming during mammalian embryonic
development, parental imprinting, and differentiation
- explain how non-protein encoding RNAs can affect gene expression
- explain the various types of RNA processing and post-transcriptional
regulation of gene expressing and design experiments to study these
- apply currently-used experimental approaches and techniques to perform
gene specific and genome-wide expression studies

Course Content

To achieve the course objectives, the following topics will be

Transcriptional regulation and Epigenetic mechanisms:
• Genome content and organization: coding versus non-coding sequences
• Composition and biochemistry of basic transcription machinery
• General and specific transcriptional regulators, their functions and
modes of regulation
• Transcription initiation, elongation and termination
• Identification and function of regulatory sequences: promoters,
enhancers, boundaries
• Properties and regulation of RNA polymerase II
• Chromatin structure and histone modifications: writers-readers-erasers
• The various DNA modifications, their biochemical properties, and role
in gene expression
• Epigenetic reprogramming during mammalian development
• Monoallelic gene expression and its importance for embryonic
development and other biological processes
• 3D Nuclear structure and long range DNA interactions
• Transcriptional regulation and chromatin changes in stem cells, during
differentiation, and development
• Cellular memory: establishing and maintenance of differentiation
• Regulatory networks: the various ways by which regulators themselves
are regulated
• Short and long non-coding RNAs and the mechanism by which they affect
gene expression
• Experimental approaches and Techniques to study gene expression,
differentiation and homeostasis

Post-transcriptional regulation:
• integration of transcriptional and post-transcriptional control
• RNA processing, including alternative splicing, and its regulation
• Nucleo-cytoplasmic RNA transport
• RNA stability and degradation pathways
• Translation regulation and RNA degradation by micro(mi)RNAs
• RNA-editing and its biological importance
• Experimental approaches and Techniques to study post-transcriptional
regulation of gene expression

Teaching Methods

- Interactive Lectures, including lectures by guest speakers (ca 45 hr).
- Web-lectures by experts (ca 5 hr)
- Self study (ca 100 hr)

Method of Assessment

There are 2 partial exams:
- First exam is halfway the course and consists of ~70-80 Multiple
Choice question and accounts for 40% of the final mark
- Second exam is at the end of the course and consists mainly of open
questions and accounts for 60% of the final mark.
For the second exam, knowledge of the first part is needed. An
insufficient grade for the first can be compensated by a sufficiently
high grade for the second and vice versa.
Resit of a partial-exam is not allowed. Pass with >5.5.

Entry Requirements

Basic concepts in Molecular Biology, Genetics, and Biochemistry


• Book: 'Gene Control' 2nd edition, by David Latchman, Garland Science
• Research and Review articles on specific topics, illustrating the
latest developments in the field (from CANVAS site)
• PPT - lecture notes

Target Audience

Master students: Biomolecular Sciences, Biology, Biomedical Sciences,
Pharmaceutical Sciences, and Cardiovascular Research

Additional Information

Compulsory portal course for MSc students Biomolecular Sciences, all

Custom Course Registration

Enrollment through studentportal:

General Information

Course Code AM_470614
Credits 6 EC
Period P1
Course Level 400
Language of Tuition English
Faculty Faculty of Science
Course Coordinator dr. J.M. Kooter
Examiner dr. J.M. Kooter
Teaching Staff dr. J.M. Kooter

Practical Information

You need to register for this course yourself

Last-minute registration is available for this course.

Teaching Methods Lecture, Study Group
Target audiences

This course is also available as: