Genomes and gene expression

Dit vak wordt in het Engels aangeboden. Omschrijvingen kunnen daardoor mogelijk alleen in het Engels worden weergegeven.

Doel vak

Course objectives:
The student is able 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

Inhoud vak

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 of
gene expression
• RNA processing, including alternative splicing, and its regulation
• Stability, translation regulation and RNA degradation by micro(mi)RNAs
• RNA-epigenetics and its biological importance
• Experimental approaches and Techniques to study post-transcriptional
regulation of gene expression


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


There are 2 partial exams:
- First exam is halfway the course and consists of ~70-80 Multiple
Choice questions 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.

Vereiste voorkennis

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


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

Overige informatie

Compulsory portal course for MSc students Biomolecular Sciences,
specialization Molecular Cell Biology and Biological Chemistry.
Students of the specialization Molecular Bioinformatics can either
choose this course as the compulsory portal course or as an elective

Afwijkende intekenprocedure

Enrollment through student portal:

Algemene informatie

Vakcode AM_470614
Studiepunten 6 EC
Periode P1
Vakniveau 400
Onderwijstaal Engels
Faculteit Faculteit der Bètawetenschappen
Vakcoördinator dr. J.M. Kooter
Examinator dr. J.M. Kooter
Docenten dr. J.M. Kooter

Praktische informatie

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Werkvormen Deeltoets extra zaalcapaciteit, Hoorcollege, Werkgroep

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