Seminar Syllabus for Biology 164: Genetic Regulation in
Eukaryotes, 2008.
Web page: http://pages.pomona.edu/~llh04747/genreg.html
In this class, each
class has a discussion leader but all students need to be prepared thoroughly
to discuss the experimental procedures and results in the paper assigned. Discussion will not use PowerPoint. The discussion leader will email questions
for discussion to the class the day before the discussion. Only the paper(s) for discussion will be
discussed in detail, but you should make sure you’ve used the background
materials to clearly understand the paper assigned for discussion. If you have trouble obtaining the pdf for an
assigned paper, please let Dr. Hoopes know.
While you’re preparing for class discussion, either as leader or
participant, Dr. Hoopes would love to discuss new methods or ideas with you to
help you get them clearly in mind. Please
bring a paper copy of the paper (or Latchman’s book if the paper is included in
it) and the questions to class. If the figures are in color, either print them
in color or make notes of the colors on the b & w print. Assigned paragraphs (see below) will be
counted towards class discussion. The
project to choose the most aesthetically appealing paper we’ve presented also
counts in this category.
There are no
examinations. There is one research paper
due about 2/3 of the way through the semester.
Lab work will be a class project, chosen in week 2, after assigned
reading and discussion. Lab meets Weds
1:15-5:30 in RCS007. Lab books are
graded twice during the semester, and must include background material you look
up on each experiment. When the lab book
is graded, part of the credit is based on effective and prepared laboratory
participation. Thus the final grade is
based on leading and participating in class discussion and on the paper and lab
grades.
WEEK 1: Tues, January 22.
Organization and
background discussion. Topics of the
course: transcriptional regulation and post-transcriptional stability of mRNA,
chromatin structure, and transcription factors. Discussion of the ways we will deal with these
topics throughout the semester. Discussion of what makes a paper ‘beautiful
work’ and development of first list of aesthetic criteria (will be revised
periodically during the semester). Preview of laboratory work. Sign up to lead discussions for sessions
through the beginning of the third week.
Thurs, Jan 24,
Lecture/Discussion. Eukaryotic
regulation overview.
Differences between prokaryotic
and eukaryotic regulation. K Struhl, Fundamentally different logic
of gene regulation in eukaryotes and prokaryotes. Cell 98:1-4
(1999). LH leads
discussion.
WEEK 2: Tues, Jan 29. Topic: Major theme
of class: Regulation by Transcription. Skim Latchman section 1 and 2 (up to p 60). Also read for
background: Gerhold et al., DNA chips: promising toys have become
powerful tools, Trends in Biochemical Sciences 24:168-173. Read
carefully for discussion: White et al., Microarray analysis of Drosophila
development during metamorphosis. Science 286:2179-2184 (1999). Bring to class a paragraph summarizing
White et al.'s findings about particular groups of genes and giving
examples of the genes in each group. Discussion
leader:
Thurs, Jan 31 Topic:
Post-transcriptional genetic regulation.
First
example: alternative splicing of
precursor RNAs. For background, read section 3 in Latchman plus Sorek, R and
Amital, M. Piecing together the
significance of splicing, Commentary. Nature
Biotech 19:196 (2001). Read
carefully for discussion Crenshaw, p71, on neuron-specificity in RNA
processing. Also read Celotto and
Graveley, Alternative splicing of the Drosophila Dscam Pre-mRNA is both
temporally and spatially regulated. Genetics
159:599-608 (2001) and Kwan, T,
Benovoy, D, Dias, C, Gurd, S, Provencher, C, Beaulieu, P, Hudson, T, Sladek, R,
and Majoewski, J. Genome-wide analysis
of transcript isoform variation in humans.
Nature Genetics Jan 2008,
online release in advance of publication, 7 pp (find on PubMed). Bring
to class one or two paragraphs summarizing the evidence used by each of these
authors and how it supports their hypotheses. Sign up to lead discussions for rest of
semester.
Discussion leader:
WEEK 3, Tues, Feb
5, Discussion. Continued discussion of post transcriptional
regulation of gene expression. Example of
translation product controlling mRNA stability.
Reread the commentary
on section 4 in Latchman and read carefully for discussion Yen et al.,
p93, on the stability of tubulin mRNA. Bring a paragraph summarizing the difference between the
mechanism described in this paper and that in the Casey et al. paper in
Latchman (which will not be discussed in class).
Begin to define a paper topic and prepare to hand in materials due next
week by choosing a research paper (not a review article) you would read for
that topic. Suggested topics, ideas, etc for your 10 page term
paper are given at a clickable site under the course web page. Discussion
leader:
Thurs, Feb 7, Day to work on paper topic and first
reference, due next week. The paper gives
each student a chance to explore in some depth a topic not covered in class, or
one that is covered but with different literature as the basis for
consideration. The purpose of the paper
is to show skill in analysis and interpretation of literature and in proposing
openings for further experimentation. The
paper will be 10-12 pages long and will evaluate in detail (similar to our
class discussions) five research papers on related topics on a subject relevant
to the class. The instructor would love to discuss your ideas for topics with
you, and may be able to suggest resources you could evaluate for use. None of the five focus papers may be ones
will have discussed or will discuss, and none may be a review article. However, you may use one or more review
articles for background and/or interpretation, in addition to the five focus
papers. Next week, you will hand in the
proposed topic and the complete reference (COMPLETE = all authors, title,
journal, volume, pages, year) for one of the five papers you’ll use.
WEEK 4: Tues, Feb 12,Discussion.
Continued post-transcriptional regulation. RNAi inhibition of mRNA usage. Read for
background, these reviews: Fire, AZ. Gene Silencing by double-stranded RNA. (Nobel lecture). Cell Death Diff 14 (12): 1998-2012 (2007) and Mello, CC, Return to the RNAi World (Nobel Lecture). Cell
Death Diff 14 (12): 1023-2020 (2007).
Read carefully for discussion this paper: Knight and Bass,
A role for the RNAse III enzyme DCR-1 in RNA interference and germ line
development in Caenorhabditis elegans. Science 293:2269-2271 (2001). Discussion leader:
Thurs, Feb 14, Discussion. Topic
transition day. First topic retrospective: gene expression by transcription
and post-transcriptional regulation, group discussion leader LH.
Note that the class will discuss and
connect the articles in this section, and will devise ‘next experiments’ that
could be done to push this field forward.
Bring to class a paragraph answering these questions: For these
two topics, what's the state of our understanding of the field as shown in the
readings? What areas are still unknown or unclear? What kinds of
experiments would be good to do now? DUE: PAPER TOPIC AND FOR ONE ARTICLE, ALL
BIBLIOGRAPHIC DETAILS (authors, complete title, journal, volume, pages, year) Please do not choose a
review article; you may use and cite review articles when writing the paper
itself, but the five articles on which the paper is based may NOT include any
review articles.
Also, Lecture/Discussion on new topic: Chromatin
structure and epigenetic regulation. Read for
background: “Chromatin Rules”, a short review by Roger Kornberg and Yahli
Lorch, Nature Struct & Molec Biol
14 (11):986-8 (2007) LH leads lecture/discussion. If time permits, we will
revise/update our criteria for aesthetically appealing papers in light of those
read to date and nominate ones from the group completed.
WEEK 5: Tues, Feb 19, NEW
TOPIC: Chromatin structure and epigenetic regulation; chromatin remodeling. Read commentary on
section 5 and review article by Berger and Felsenfeld, Chromatin
goes global, Molecular Cell 8:263-8
(2001). Read and prepare to discuss: Kwon et
al., Nucleosome disruption and enhancement of activator binding by a human
SWI/SNF complex. Nature
370:477-481 (1994); Bochar et al., BRCA1 is associated with a human
SWI/SNF-related complex: linking chromatin remodeling to breast cancer. Cell 102:257-265 (2000); and Lee, W, Tillo, D, Bray, N, Morse, R,
Discussion leader:
Thurs, Feb 21,
Discussion. Chromatin
structure and epigenetic regulation, RNAi role and matrix interactions. Read for nuclear
organization background, Sexton, T, Schober, M,
Fraser, P, and Gasser, SM. Gene
Regulation Through Nuclear Organization.
Nature Structural & Molecular
Biology 14 (11):1049-1055 (Nov, 2007.) Read carefully for discussion.
Buhler,
M and Moazed, D. Transcription and RNAi
in heterochromatic gene silencing. Nature Struct & Mol Biol 14
(11):1041-1048 (Nov, 2007) and Cai,
S, Han, H-J, and Kohwi-Shigematsu, T. Tissue-specific nuclear
architecture and gene expression regulated by SATB1. Nature Genetics 34:42-51 (2003).
Discussion leader:
WEEK 6: Tues, Feb 26.
Discussion. Chromatin;
DNA methylation.
Reread commentary on section 5 and read the review article by Rhazin,
CpG methylation, chromatin structure and gene silencing--- a three-way
connection. EMBO Journal 17:4905-4908
(1998) and skim the review article by Gronbaek,
K, Hother, C and Peter A Jones, Epigenetic changes in cancer, APMIS 115:1039-1059 (2007) for
background. Read for discussion: McGhee and Ginder, p 125 in
Latchman, on the role of DNA methylation in regulation of chicken hemoglobin
gene expression, Zhang, Q., Wang, H, Marzer, M, Raghunath,PN,
Nagasawa, T and Waski, M. STAT3-and DNA
methyltransferase 1-mediated epigenetic silencing of SHP-1 tyrosine phosphatase
tumor suppressor gene in malignant T lymphocytes. Proc
Natl Acad Sci USA 102:6948-53 (2005) and Linhart,
H, Lin, H, Yamada, Y, Moran, E, Steine, E, Goldhale, S, Lo, G, Cantu, E,
Ehrich, M, He, T, Meissner, A, and Jaenisch, R
Dnmt3b promotes tumorigenesis in vivo by gene-specific de novo
methylation and transcriptional silencing.
Gene & Devel. 21:3110-3122 (2007).
Discussion leader:
Thurs, Feb 28, Discussion. Chromatin,
imprinting. Read for
background Allshire and Bickmore, Pausing for thought on the boundaries
of imprinting. Cell 102:705-708
(2000), the detailed drawings in Lall, S. Primers on Chromatin. Nature
Struct & Molec Biol
14:1111-1115 (Nov, 2007), and Hore,
T, Rapkins, R, and Marshall Graves, JA.
Construction and evolution of imprinted loci in mammals. Trends
in Genetics 23 (9): preprint, 9 pp, pdf available through ScienceDirect on
PubMed. Read carefully for discussion the article by Khosla
et al, Parental allele-specific configuration in a boundary-imprinting-control
element upstream of the mouse H19 gene. Molec and Cell Biol 19:2556-2566 (1999); Bourc'his, D,
Xu, GL, Lin, CS, Bollman, B, Bestor, T, Dnmt3L and the establishment of
maternal genomic imprints. Science 294:2536-2539
(2001). Discussion leader:
WEEK 7: Tues, Mar 4 ,
Discussion. Chromatin;
X-inactivation.
Read for introduction: Heard, E. Recent
advances in X-chromosome inactivation.
Current Opinion in Cell Biology 16:247-255 (2004). Read for discussion:
Hernandez-Munoz,
Thurs, Mar 6. Discussion. Chromatin:
Histone acetylation and methylation. Reread Struhl for background and Feinberg, AP, Phenotypic plasticity and the epigenetics of human
disease. Nature 447: 433-440 (May, 2007).
Figure 1 is especially useful. Read
carefully for discussion Kuo et al, Genes
Dev. 12:627-639 (1999), on action of the Gcn5 histone acetylase near an
active promoter, Litt et al., Correlation between histone lysine methylation and
developmental changes at the chicken globin locus. Science 293:2453-2455 (2001), and Pal-Bhadra, M., et al., Heterochromatic
silencing and HP1 localization in Drosophila
are dependent on the RNAi machinery, Science
202:669-672 (2004).
Discussion leader:
WEEK 8: Tues, March
11, Topic transition. Second topic retrospective:
chromatin and epigenetic regulation, Bring to class a paragraph answering these
questions: For this topic, what's the state of our understanding of the field
as shown in the readings? What areas are still unknown or unclear?
What kinds of experiments would be good to do now? Group discussion
leader: LH. Also, Short Lecture/discussion on new topic: DNA
Binding Sites for Regulatory Proteins: Promoters and enhancers. LH.
Thurs, Feb 13. No class.
Use time to find the rest of your articles for the paper and begin to
analyze them.
WEEK OF MAR 18-20: Spring break, no
classes.
WEEK 9: Tues, March 25. Discussion. DNA Binding Sites: Promoters and
Enhancers. For
background, read Latchman
commentary 7 and Iyer et al, Genomic binding sites
of the yeast cell-cycle transcription factors SBF and MBF. Nature 409:533-538 (2001) (found at http://genome-www.stanford.edu/chromatinip/sbfmdf.pdf ); for discussion read the Hanahan paper, p 173, on pancreatic
tumorigenesis in transgenic mice caused by an enhancer being attached to an
oncogene. Discussion
leader:
Thurs, March 27. Discussion, RNA Polymerase II; general
and specific transcription factors. Read for background, Goodrich
et al, Contacts in Context: Promoter specificity and macromolecular
interactions in transcription. Cell
84:825-830 (1996). Discuss as overview, Cramer
et al., Structural basis of transcription: RNA polymerase II at 2.8 Angstrom
resolution. Science 292:1863-1882
(2001). Discuss in detail: Li et al., Distinct classes of
yeast promoters revealed by differential TAF recruitment, Science 288:1242-1244 (2000) and Tamkun, JW, Stalled polymerases and transcriptional regulation. Nature Genetics 39: 1421-22 (2007). Discussion
leader:
WEEK
10. Tues, Apr 1. Discussion. Specific Transcription Factors. Purification and characterization. For background, carefully read the Latchman commentary on section 8 and the review article, Kadonaga, JT, Regulation of RNA
Polymerase II transcription by sequence-specific DNA binding factors. Cell 116:247-257. Read carefully for presentation both the Kadonaga
and Tjian paper, p 195, on the first purification of a transcription
factor, and the paper by Kadonaga et al., p 201, on the functional
analysis of the Sp1 transcription factor. Discussion leader:
Thurs, Apr 3 Discussion, Transcription
factors, structure and action. For background, skim the article by Kissinger et al, p 223, on the x ray crystallography
of the complex of the engrailed protein homeodomain and the DNA to which it
binds. Read carefully for discussion Passner et al. Structure of a
DNA-bound Ultrabithorax-Extradenticle homeodomain complex. Nature 397:714-719, (1999) and Muse, G, Gilchrist D, Nechaev, S, Shah,
R, Parker, J, Grisson, S, Zeitlinger, J, Adelman, K. RNA Polymerase is poised for activation
across the genome. Nature 39:1507-1511 (2007). Discussion
Leader:
Week 11, Tues Apr 8. Discussion. Cont: Transcription factors: protein
interaction. Read for background, commentary for section 10 in Latchman.
Read carefully for discussion Landschutz et al, p 237, on dimerization
via the leucine zipper structure, Gonzalez and Montminy, Latchman p 257,
on control of the CREB transcription factor via phosphorylation controlled by
cAMP levels, and Barone, MV,
Pepperkok, R, Peverali, F, and Philipson, L.
Id proteins control growth induction in mammalian cells. Proc
Natl Acad Sci
NOTE: Paper is due next Tuesday. Paper
is to be about 10 pp of text, with copied figures added as needed to make the
discussion clear to the reader. Paper is to be an in depth analysis
of 5 related papers (one of which was reviewed and approved when you
submitted earier) from the recent literature on an approved topic. The
paper introduction should highlight the relationship of the area chosen to
other topics covered in the course, the main body should examine the logic of
the experiments done by each team and the support they provide for the
hypotheses (very similar to class discussions we have had), and in conclusion,
should discuss the relationship between the findings in the various papers and
additional experiments that would clarify the findings. The best papers
will give approximately equal treatment to each of the 5 main articles on which
the analysis is based. If appropriate, your conclusion should
include your model of how the regulatory system under study appears to
work. Complete and accurate bibliographic information should be presented
in the style used by the journal Molecular and Cellular Biology.
Thurs, Apr 10. Discussion, Transcription factors, cont. Read for
background the commentary to section 12 in Latchman and read carefully for
discussion Kaffman et al., The receptor Msn5 exports the
phosphorylated transcription factor Pho4 out of the nucleus. Nature
396:482-486 (1998) and Martinez-Garcia et al., Direct targeting of
light signals to a promoter element-bound transcription factor. Science
288:859-891 (2000). Discussion
leader:
WEEK 12, Apr 15,
Discussion, Transcription factor regulation, stem cells.
Read for discussion Mitsui, K, Tokuzawa, Y, Itoh, H, Segawa, K,
Murakami, M, Takhashi, K, Maruyama, M, Maeda, M, and Yamanaka, S. The
homeoprotein Nanog is required for maintenance of pluripotency in mouse
epiblast and ES cells. Cell 113:631-642
(2003) and Takahashi, K, Tanabe, K,
Ohnuki, M, Narita,M, Ichisaka, T, Tomoda, K, and Yamanaka, S. Induction of Pluripotent Stem Cells from
Adult Human Fibroblasts by Defined Factors.
Cell 131: 1-12 (Nov, 2007) Discussion leader:
Thursday, Apr 17: PAPER IS DUE IN CLASS
TODAY!! Discussion, Transcription factors. Reread Latchman's commentary
to sections 12 and 13, and read for discussion Baurle and
Baltimore, p 263, on a
specific inhibitor of the transcription factor NF-KB that regulates expression
of antibody genes and Henry and Melton, Mixer, a homeobox gene required for endoderm development, Science 281:91-96 (1998). Discussion leader: Laura Hoopes
WEEK 13, Tuesday, Apr 22, Discussion, transcription
factors and other mechanisms in cancer and aging. Read
for background, Greer, EL and
Brunet, A, FOXO transcription factors in ageing and cancer. Acta
Physiol 192:19-28 (2008). Read
carefully for discussion, Hwangbo DS,
Gershman B,
Tu MP,
Palmer M,
Tatar M,
Drosophila dFOXO controls lifespan and regulates insulin signaling in
brain and fat body. Nature 429:562-6 (2004). Timofeeva, O, Gaponenko, V, Lockett, S,
Tarasov, S, Jiang, S, Michejda, C, Perantoni, A, and Tarasova, N. Rationally
Designed Inhibitors Identify STAT3 N-Domain as a Promising Anticancer Drug
Target. ACS Chemical Biology 2:799-804 and Kumar, M, Lu, J, Mercer, K, Golub, T, and Jacks, T. Impaired microRNA processing enhances
cellular transformation and tumorigenesis.
Nature Genetics 39:673-677 (May, 2007). Discussion leader:
Thursday, Apr 24,
Retrospective on RNA Polymerase II (mRNA), transcriptional Regulation via
promoters/enhancers, and transcription factors, group discussion leader LH.
Bring to class a paragraph answering these questions: For this topic group,
what's the state of our understanding of the field as shown in the readings?
What areas are still unknown or unclear? What kinds of experiments would
be good to do now? Also: planning for class discussion of the
contenders for “Most Aesthetic Paper of the Year.”
Week 14: Tuesday, April 29, Discussion
of papers written by the students in the class, informal, with refreshments.
Thurs, May 1: Discussion.
MANDATORY CLASS!! If you
must miss this class, you must make prior arrangements. Retrospective overall discussion of the
class, examining the approaches used, the overall picture of eukaryotic
regulation developed, and the excellence of the papers reviewed (personal
aesthetic appreciation required!). The
Most Aesthetic Paper of those we
discussed will be voted upon and posted on the internet today.
NO FINAL EXAMINATION, HAVE A Great Commencement or a GREAT BREAK!