BIOLOGY 463 - GENE REGULATION IN DEVELOPMENT
Instructor: Dr. Bob Argiropoulos
Lectures: Mon., Wed., Fri. 9 to 10AM Wesbrook Rm 201
Office: Hut B6, Room 1
Office hours: Mon., Wed., Fri. 11AM to 1PM OR By appointment
email: bargirop@zoology.ubc.ca
Grading: 40% Critical review literature assignment (Oral and written presentations)
20% Midterm exam - Friday, October 10th, 2003
40% Final exam - Friday, December 5th, 2003, 3:30 pm, BioSci Rm 2000
Textbook: The textbook for this course is entitled "Molecular Principles of Animal Development" and is authored by Alfonso Martinez Arias and Alison Stewart. Although this book is highly recommended, it is not required. Alternatively, the developmental biology chapters in "Molecular Biology of the Cell" by Alberts et al. and "Genetic Analysis" by Griffiths et al. can provide some background information.
Prerequisites: Prerequisites are BIOL 335 (Molecular Genetics) and one of BIOC 300, 302 or 303 (Biochemistry). BIOL 331 (Developmental Biology) is recommended. Companion courses include BIOL 331, 432, 441, 452, 464.
COURSE OUTLINE
1) Course Introduction
Development
Structure and function of DNA
2) Transcriptional Regulation
The mechanics of gene expression
Transcription factors
Enhancer design
3) Establishing the anterior-posterior pattern in Drosophila
4) Axis formation in Drosophila: the dorsal/ventral axis
5) The design of developmentally regulated enhancers
COURSE OBJECTIVES
The molecular basis of determination of cell fate is of great importance in understanding the development of higher organisms. Determination is controlled by a complex network of transcription factors whose expression patterns are tightly regulated. To understand determination it is essential to understand the molecular mechanisms of this transcriptional network. Much of the information that determines the spatial and temporal expression pattern of transcription factors encoded in an organism's DNA via sophisticated cis-regulatory sequences. Deciphering how these cis-regulatory sequences control gene expression is key to understanding development and the focus of this course.
The overall aim of this course is to teach you how developmentally regulated enhancers decipher regulatory inputs and generate novel regulatory outputs. We will explore development from the point of view of the molecules and the processes that are involved in the shaping of embryos, rather than from the point of view of the organism. By the end of the course you will have a better understanding of how transcription factors bind enhancers, what happens when they get there and how these events are translated into the formation of a complex organism.
There are a number of more general aims. You will learn to analyze and critically review scientific papers. To do this, you must learn the current techniques of molecular biology. Although this is not a methods course, you will notice that we spend a considerable amount of time discussing them. The reason being that if you do not know the methods, you cannot understand the experiments.
Ultimately, the main goal of this course is to teach you to think like a scientist. Hopefully you will learn how to ask meaningful biological questions, to devise experiments that directly test this question, to interpret results, and to use the data to generate working models.
This course will greatly benefit students interested in genetics, developmental biology, molecular biology/biotechnology, and medicine. This is a non-laboratory course.
Succeeding in the course
This is a 400-level course and it will be taught at a rigorous level. Since this is a biology course, a major goal is to encourage you to "think biologically," with understanding rather than dependence on note memorization. You will need to know some basics but much of the time will be spent thinking about how to solve a biological problem. This means that you need to study in a different way, since memorizing your notes will not help you very much. Although not strikingly obvious, everything taught in this course is connected. Your ability to make connections between otherwise unrelated material taught at different parts of the course is key. When pondering over your notes you should be asking yourself "Why am I being told this?" "Have I seen something similar before?" "What is the fundamental principle?"
I strongly advise you to come prepared for each class. Read the papers before they are discussed in class and I strongly urge you to participate in class discussions.
LECTURE NOTES
Lecture 1. Wed., Sept. 3rd, 2003 - Introduction to gene regulation in development
Lecture 2. Fri., Sept. 5th, 2003 - Gene structure
Lecture 3. Mon., Sept. 8th, 2003 - Transcription and Chromatin
Lecture 4. Wed., Sept. 10th, 2003 - Measuring gene expression
Lecture 5. Fri., Sept. 12th, 2003 - Regulation of the b-globin locus (Appendix 1 - ChIP)
Lecture 6. Mon., Sept. 15th, 2003 - Regulation of the b-globin locus
Lecture 7. Wed., Sept. 17th, 2003 - Structure of transcription factors & DNA binding (Appendix 2)
Lecture 8. Mon., Sept. 22nd, 2003 - Transcription factor dimerization and its consequences: Jun & Fos
Lecture 9. Wed., Sept. 24th, 2003 - Jun & Fos Continued
Lecture 10. Fri., Sept. 26th, 2003 - Versatility of POU proteins
Lecture 11. Mon., Sept. 29th, 2003 - Basis for HOX specificity
Lecture 12. Wed., Oct. 1st, 2003 - Basis for HOX specificity continued
Lecture 13. Fri., Oct. 3rd, 2003 - Introduction to Drosophila development and genetics
Sample examination question - Appendix 3
Lecture 14. Mon., Oct. 6th, 2003 - Introduction to Drosophila development and genetics
Lecture 15. Wed., Oct. 8th, 2003 - Review for Midterm examination
Midterm examination - Fri., Oct. 10th, 2003
Lecture 16. Wed., Oct. 15th, 2003 - Anterior-Posterior axis formation in Drosophila
Lecture 17. Fri., Oct. 17th, 2003 - Regulation of even-skipped stripe 2 in the Drosophila embryo
Lecture 18. Mon., Oct. 20th, 2003 - Regulation of even-skipped stripe 2 in the Drosophila embryo
Lecture 19. Wed., Oct. 22th, 2003 - Transcriptional synergy at eve stripe 2 enhancer
Lecture 20. Fri., Oct. 24th, 2003 - Review/discussion of last three eve papers
Lecture 21. Mon., Oct. 27th, 2003 - Position-specific repression of eve stripe 2
Lecture 22. Wed., Oct. 29th, 2003 - Position-specific repression of eve stripe 2
Lecture 23. Fri., Oct. 31st, 2003- The homeotic genes
Lecture 24. Mon., Nov. 3rd, 2003 - Regulation of homeotic gene expression (Appendix 4)
Lecture 25. Wed., Nov. 5th, 2003 - The biology of maintenance elements
Lecture 26. Fri., Nov. 7th, 2003 - Dorsal-ventral axis formation in Drosophila
Lecture 27. Wed., Nov. 12th, 2003 - Bioinformatics and Systems Biology
Classroom Presentations begin on Fri., Nov. 14th, 2003
This site is maintained by
Dr. Bob Argiropoulos. It was last updated on November 10th, 2003. If you
have any comments or suggestions please send email to: bargirop@zoology.ubc.ca