Code: BIOL-475
Semester: H
Course Type: Elective
ECTS units: 5

Instructor

photo dkp

Associate Professor: Papadopoulos Dimitrios
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Office phone number: +30 2810 394353
Lab phone number: +30 2810 394352

Description

Objectives of the course (preferably expressed in terms of learning outcomes and competences): The lecture aims at explaining the transcription factor biophysical properties which determine organismal development, the control of gene expression, as well as human disease. The methodologies deployed for the measurement of the concentration and kinetics of transcription factors in live cells, as well as transcription factor labelling technologies, will be taught in such a fashion that allows a profound understanding of transcription factor behavior during development, while promoting the critical thinking and problem-solving abilities of the students. An interdisciplinary way of thinking will be developed during the course by combining the knowledge required for the understanding of processes related to chemical kinetics, biophysics, molecular and developmental biology, biochemistry, and protein engineering.

Course contents:

1. Transcription factor molecular families

2. Basic problems in the study of transcription factor dynamic behavior (abundance/concentration, diffusion, affinity, chromatin-binding kinetics, variability)

3. Methodologies for the study of transcription factor biophysical behavior

4. Transcription factor–chromatin-binding kinetics

5. Means of transcription factor binding site acquisition on enhancers; interactions with RNA Polymerase II

6. Functional differences in the binding site acquisition processes exhibited by transcription factors in prokaryotic vs. eukaryotic genomes

7. Cell-to-cell variability in the abundance of transcription factors

8. Intrinsic and extrinsic transcriptional noise

9. Control of noise (variability) in transcription factor concentration during development, differentiation, and organismal physiology

10. Formation of biomolecular condensates (phase separation)

11. Human diseases that depend on transcription factor concentrations

12. Degeneration of neuronal cells; neurodevelopmental diseases (FUS/TDP43)

13. Molecular “grammar” of amino acids participating in the formation of biomolecular condensates; agent and client proteins in condensates; the role of RNA

14. Regulation of transcription factor concentration through the formation of biomolecular condensates