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Molecular Systems Biology Practical course



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Prof. U. Gaul UG
Dr. Ch. Jung ChJ


Molecular systems biology practical course

The students will learn how to develop efficient high throughput assays and how to analyse the data coming from such experiments. The three week course will cover the following topics:

1) A high throughput dual luciferase assay to measure the activity of Drosophila core promoters. Students will experience working with a robot and will first carry out a 96-well plate plasmid preparation, measure the DNA content, set up transient transfections in S2 cells and measure the dual luciferase assay. The students will learn which problems were associated with developing these assays and spend two days doing a thorough data analysis.

2) A high throughput assay to measure the binding affinity of transcription factors. The students will again learn how to develop such an assay and which pitfalls to avoid. The assay based on fluorescence anisotropy, and combines a competition assay with a controled delivery system, such that one can measure many different competitor concentrations in one well. A fully developed pipeline will be used, from the assay to the data analysis.

3) The students will measure nucleosome positions, occupancy and fragility genome-wide using MNase digestion. Mnase titration experiments can determine whether a nucleosome is fragile (enhancers and promoters) or whether it is resistant (gene body). Nucleosome mapping will be carried out experimentally and computationally, where the students will correlate the fragility of nucleosomes with GC content, position in the genome, and activity of the genes.