Genomes and gene expression

2018-2019
Dit vak wordt in het Engels aangeboden. Omschrijvingen kunnen daardoor mogelijk alleen in het Engels worden weergegeven.

Doel vak

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
tissues
- 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
processes
- 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
discussed:

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
concept
• 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
status
• 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

Onderwijsvorm

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

Toetsvorm

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.

Vereiste voorkennis

Basic concepts in Molecular Biology, Genetics, and Biochemistry

Literatuur

• 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

Doelgroep

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

Overige informatie

Compulsory portal course for MSc students Biomolecular Sciences, all
specializations.

Afwijkende intekenprocedure

Enrollment through studentportal: Vunet.vu.nl

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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