Schedule for 501 Sect. 3 Gene Expression 2015
Section Director, W.K. Samson Ph.D., D.Sc. samsonwk@slu.edu
Meets in LRC106 from 9-10 AM or from 9-11 AM on dual lecture days
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Lecture Date
Thursday, October 8
9-10 AM
Friday, October 9
9-10 AM
Monday, October 12
9-10 AM
Tuesday, October 13
9-10 AM
Wednesday, October 14
9-10 AM
Thursday, October 15
9-10 AM
Friday, October 16
9-10 AM
Monday, October 19
9-10 AM
Tuesday, October 20
9-10 AM
Wednesday, October 21
9-10 AM
Thursday, October 22
9-10 AM
Friday, October 23
9-10 AM
Friday, October 23
10-11 AM
Monday, October 26
9-10 AM
Tuesday, October 27
Wednesday, October 28
Lecturer
Lecture Title
Zassenhaus
Overview and Bacterial Gene Expression
Zassenhaus
Bacterial Gene Expression
Zassenhaus
Bacterial Gene Expression
Zassenhaus
Prokaryotic/Eukaryotic Gene Regulation
Chang
Protein Synthesis I
Chang
Protein Synthesis II
Skowyra
Protein Folding and Quality Control
Skowyra
Skowyra
Targeted Proteolysis as a Main Regulatory
Mechanisms of Gene Expression I
Targeted Proteolysis as a Main Regulatory
Mechanisms of Gene Expression II
Eliceiri
RNA Processing
Eliceiri
Micro RNAs and RNAi
Eissenberg
Chromatin Structure and Transcription I
Eissenberg
Chromatin Structure and Transcription I
Eissenberg
Transcriptional Repression
Study Day
9-Noon
Exam
Revised 9/17/2015
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Section on Gene Expression
Transcriptional Regulation
Thursday, October 8– Tuesday, October 13
Zassenhaus, Doisy Research Center,
Zassenp@netscape.net
Part I: Bacterial Transcriptional Regulation Oct 8-12
Readings: Handed out as text is Chapter 1 of the book “Genes and Signals” by Mark
Ptashne and Alexander Gann. Before class on Thursday, 10/8, please read Chapter 1,
pages 11-39. This is a very readable, small page size book with lots of good figures, not
heavy on facts, but superbly rich on ideas and explanations. This one chapter explains
ALL of transcription, gene regulation, AND cell signaling in all life forms! Once you
understand the principles presented here, then all the rest is just filling in the details. Our
goal in class will be to learn those principles. Before Class on Monday, 10/12, finish
reading Chapter 1, pages 40-52. During Part 1, we will focus on how the binding
properties of transcriptional regulators determine how regulation works. Therefore, it
will be helpful if you review protein-protein interactions from earlier in the course,
particularly the quantitative aspects of measuring protein binding – i.e., the math of
binding equilibria.
Over the course of the first three lectures (Tuesday and Wednesday) we will cover:
1. Structure and function of the bacterial RNA polymerase
2. Regulated Recruitment of transcriptional regulators:
Protein-DNA Interactions
Detecting physiological signals
Cooperative binding of proteins to DNA
Turning genes on or off – activation versus repression
3. Bacteriophage Lambda
The genetic switch of lysogeny versus lytic growth
Establishing lysogeny
Making an efficient switch – the importance of cooperativety
The repressor as a gene activator
DNA binding and synergy
4. Polymerase activation: NtrC and conformational changes in pre-bound polymerase
5. Promoter activation
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Part II: Pro- and Eukaryotic transcriptional regulation (Tuesday,
October 13)
Although the principles utilized by eukaryotes to regulate gene transcription are the same
as you will have learned from examining bacterial gene regulation, the details are both
different and fascinating in their own right. Eukaryotes are also a marvelous example of
how simple principles can be combined into complex regulatory schemes. We will focus
on yeast as a model system to learn about how eukaryotes regulate gene activity. Before
class on Tuesday, please read the hand-out text which is Ptashne Chapter 2, pages 59103. In these lectures, we will focus on:
1. The structure of the eukaryote RNA polymerase machinery
2. Gal4 as a model transcriptional regulator
3. The nature of the activation domain in a transcriptional regulator
4. Recruitment of the RNA polymerase by transcriptional regulators
5. The role of nucleosomal modifiers in gene regulation
6. Transcriptional repression
7. Cooperative and combinatorial control of gene activity
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Protein Synthesis
Wednesday, October 14 and Thursday October 15
Yie-Hwa Chang, Doisy Research Center room 515, Ext. 7-9263
changyh@slu.edu
Suggested readings:
1. Cell and Molecular Biology, Kleinsmith and Kish (2nd edition), Chapter 11
2. Berg, JM, Lorsch, JR (2001) Mechanism of ribosomal peptide bond formation.
Science 291: 203
3. Ibba, M., Soll, D. (1999) Quality control mechanism during translation. Science 286:
1893
Part I: Mechanism of protein synthesis
1. Ribosome structure
2. Protein Synthesis
2.1 mRNA
2.2 tRNA
2.3 The initiation of protein synthesis
2.4 Peptide bond formation
2.6 Translocation
2.7 Termination of protein synthesis
2.8 Polysomes
Part II: The regulation of protein synthesis
Suggested readings:
1. Cell and Molecular Biology, Kleinsmith and Kish (2nd edition), Chapter 11
2. Pestova, TV, et al (2001) Molecular mechanism of translation initiation in eukaryotes.
Proc. Nat. Acad. Sci. USA 98: 7029
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3. Gale, M., Tan, S.L., and Katze M.G. (2000) Translational control of viral gene
expression in eukaryotes. Miocrobiol. Mol. Biol. Rev. 64: 239
1. Translational repressors
2. Life span of mRNA
3. RNAi
4. Phosphorylation
5. Availability of tRNA
5. Rate of termination of translation
7. Initiation factors.
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Protein Folding and Quality Control; Targeted Proteolysis as a
Main Regulatory Mechanism of Gene Expression
Friday, October 16– Tuesday, October 20
Yie-Hwa Chang, PhD., Doisy Research Center room 515, Ext. 7-9263
changyh@slu.edu
Dorota Skowyra, PhD., Doisy Research Center room 407, Ext. 7-9280
skowyrad@slu.edu
The economics of protein synthesis, folding, and degradation: the evolutionary
solutions to optimize the cost of gene expression
Reading:
(1) Yewdell, J.W. (2001): Not such a dismal science: the economics of protein
synthesis, folding, degradation and antigen processing. Trends in Cell Biology, 11(7),
294-297.
(2) Schubet, U., Anton, LO.C., Gibbs, J., Norbury, C.C., Yewdell, J.W., Bennink, J.R.
(2000): Rapid degradation of a large fraction of newly synthesized proteins by
proteasomes. Nature 404, 770-774.
Overview: Once synthesized on the ribosome, every polypeptide needs to fold into a
conformation that ensures its designed function, modification and/or interaction with
other proteins. Frequently, such conformation involves multiple independently folded
modules and is hard to be achieved by spontaneous folding of the polypeptide itself.
Indeed, in the cell, protein folding is assisted by molecular chaperones, which in
multiple rounds of ATP-dependent binding and release “massage” the protein into its
optimal shape. If this process fails, the misfolded polypeptides are recognized by cellular
quality control systems and eliminated by targeted proteolysis via the ubiquitinproteasome pathway. A proteolytic pathway that recognizes and destroys abnormal
proteins must be able to distinguish between completed proteins that have “wrong”
conformations and the many growing polypeptides on ribosomes that have yet not
achieved their normal folded conformation. That this is not a trivial issue is
demonstrated by the observation that in normal growth conditions approximately one
third of newly synthesized proteins are degraded within minutes of their synthesis (Ref
2). Is this the best evolutionary solution to the problem of optimizing the cost of a
successful expression of a given gene? We will discuss this issue in class. PLEASE,
READ THE SUGGESTED LITERATURE AND PREPARE FOR DISCUSSION.
Problem (prepare your opinion to discuss in class): In your opinion, is the high rate of
degradation of the newly synthesized proteins the best solution to the problem of
optimizing the cost of a successful gene expression?
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Ubiquitin-dependent proteolysis as a key regulator of the biological processes,
including gene expression
Reading:
(1) Selected chapters from: Glickman, M., and Ciechanover, A. (2002): “The UbiquitinProteasome Proteolytic Pathway: Destruction for the Sake of Construction”, Physiol.
Rev. 82: 373-428. Chapter I: Introduction and overview, pp. 374-376. Chapter II: The
ubiquitin conjugation machinery, pp. 377-381. Chapter IV: Modes of substrate
recognition and regulation of the ubiquitin pathway, pp. 383-388.
(2) Conaway, R.C., Brower, C.S., Weliky-Conaway, J. (2004) “Emerging roles of
ubiquitin in transcription regulation”. Science 296, 1254-1258 (read for Friday).
Overview: Between the 1960s and 1980s protein degradation was a neglected area,
considered to be a non-specific dead-end process. Although it was known that proteins
do turn over, the large extent and specificity of this process, whereby distinct proteins
have half-lives that range from a few minutes to several days, was not appreciated. The
discovery of the lysosome by Christian de Duve did not significantly change this view,
because it became clear that this organelle is involved mostly in the degradation of extracellular proteins, and their proteases cannot be substrate specific. The discovery of the
complex cascade of the ubiquitin pathway revolutionized the field. It is clear now that
degradation of cellular proteins is a highly complex, temporally controlled, and tightly
regulated process that plays major roles in a variety of pathways during cell life and
death, including the regulation of gene expression, stress and immune responses, cell
cycle control and metabolic adaptation. We will discuss how the ubiquitin-mediated
proteolysis contributes to the regulation of gene expression.
Problem (prepare your opinion to discuss in class): how would you design an
evolutionary conserved system for intracellular protein degradation which would be
required to target 80% of total cellular proteins in a specific, regulated (when needed),
and timely (fast) manner?
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RNAs: types, functions and processing
Wednesday and Thursday , October 21&22 – 9:00 – 10:00am
George Eliceiri, Doisy Hall room R522, Ext. 7-7863
eliceiri@slu.edu
Reading:
Relevant sections of chapters 6 and 7, Molecular Biology of the Cell by B. Alberts et al.
(2008).
Concepts:
Types of RNAs
protein-coding RNAs (messenger RNAs, mRNAs)
noncoding RNAs
ribosomal RNAs
transfer RNAs
spliceosomal small nuclear RNAs
small nucleolar RNAs
small interfering RNAs
microRNAs
others
Structures of RNAs
Functions of various RNAs
ribozymes
others
Processing of various RNAs
processing of termini
RNA splicing
group I intron splicing
group II intron splicing
spliceosomal splicing
nucleotide modifications
RNA editing
alternative mRNA processing
mRNA transport and localization
mRNA decay
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Chromatin Structure and Transcription
Friday, October 23 (9:00-11:00) and Monday, October 26 (9:00-10:00)
Joel Eissenberg, Doisy Research Center, Room 421, Ext. 7- 9235
Eissenjc@slu.edu
In each lecture, I’ll present some background material related to the key questions and
present experimental results from one or two research papers illustrating experimental
approaches to answering these questions.
Chromatin structure and gene activation I
All, or nearly all, of the DNA in a eukaryotic nucleus is packaged into nucleosomes.
What is a nucleosome? Do nucleosomes adopt specific positions on chromosomes to
facilitate gene regulation, or are they randomly distributed? Are nucleosomes a barrier to
transcription factor access under physiological conditions?
Readings:
Yuan, G.-C., Y.-J. Liu, M.F. Dion, M.D. Slack, L.F. Wu, S.J. Altschuler and O.J. Rando
(2005) Genome-scale identification of nucleosome positions in S. cerevisiae. Science
309: 626-630
Li, G., and J. Widom (2004) Nucleosomes facilitate their own invasion Nature Structural
Mol. Biol. 11: 763-760
Chromatin structure and gene activation II
What is the relationship between transcription factor occupancy and gene expression? Is
the affinity of a transcription factor affected by the presence of a nucleosome and vice
versa?
Reading:
Lickwar, C.R., F. Jueller, S.E. Hanlon, J.G. McNally and J.D. Lieb (2012) Genome-wide
protein-DNA binding dynamics suggest a molecular clutch for transcription factor
function. Nature: 251-255.
Chromatin modifications and transcriptional regulation
Post-translational modifications at certain sites on certain histones are correlated with
gene activation or silencing. How do different modifications affect gene expression?
Readings:
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Kuo, M.-H., J. Zhou, P. Jambeck, M. E. A. Churchill, and C.D. Allis (1998) Histone
acetyltransferase activity of yeast Gcn5p is required for the activation of target genes in
vivo. Genes Devel. 12: 627-639
Nielsen, S.J., R. Schneider, U.-M. Bauer, A.J. Bannister, A. Morrison, D. O’Carroll, R.
Firestein, M. Cleary, T, Jenuwein, R.E. Herrera, and T. Kouzarides (2001) Rb targets
histone H3 methylation and HP1 to promoters. Nature 412: 561-565.
Tuesday, October 27
NO CLASS (STUDY DAY)
Wednesday, October 28
Exam 9:00 - NOON
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