Seminar Syllabus for Biology 164: Genetic
Regulation in Eukaryotes, 2009.
Web page: http://pages.pomona.edu/~llh04747/genreg.html
Genetic regulation
is a major hot topic in biology research today.
All the cells of the body develop from a single fertilized egg cell via
genetic regulatory mechanisms. In this
class, we will focus on mechanisms that connect to production and function of
the messenger RNA and not on protein kinase signaling or other kinds of
regulatory mechanisms, although we’ll find that sometimes such other mechanisms
actually regulate the concentrations of messenger RNA, and we’ll examine some
examples.
I believe in active
learning, so this course is as close to all-discussion as I can make it. 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 because I’ve found that creates a situation where only
the presenter really understands and interacts with the material. To stimulate our thinking, the discussion
leader will email questions for discussion to me and 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.
The text is a
collection of classic papers in the field, edited by and with commentary by
David Latchman, a major figure in transcription factors: Landmarks in Gene Regulation.
If you’ve ordered the book and it is not in yet, let Dr. Hoopes know so
she can make the assigned papers available on Sakai. If you have trouble obtaining the pdf for an
assigned paper from a journal, please let Dr. Hoopes know so she can get it for
you. 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.
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. Assigned paragraphs
(see below) will be counted towards class discussion. The class chooses the most aesthetically
appealing paper we’ve presented each year and the criteria for that choice will
be discussed periodically throughout the semester.
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
Tuesdays 1:15-5:30 in RCS007. Lab books
are graded twice during the semester, and must include notes on papers for background
that you look up and read on each experiment. When the lab book is graded, part of the
credit is based on effective and prepared laboratory participation, part on
accurate, dated, complete lab notes, and part on well-supported conclusions
drawn. Thus the final grade is based on
leading and participating in class discussion and on the paper and lab grades.
WEEK 1: Tues, January 20.
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 22, Lecture/Discussion. Eukaryotic regulation overview. Differences between
prokaryotic and eukaryotic regulation. Background, L Hoopes, www.nature.com/scitable, Gene expression and regulation. Nature
Education 1(1), (2008); read for discussion K Struhl,
Fundamentally different logic of gene regulation in eukaryotes and
prokaryotes. Cell 98:1-4 (1999). LH leads discussion.
WEEK 2: Tues, Jan 27. Topic: Major theme
of class: Regulation by Transcription. Skim Latchman’s
introductions in section 1 and 2 (only up to p 60). Also read for
background: Scitable (see site above): Phillips, T. Regulation of transcription and gene
expression in eukaryotes. Nature Education 1(1), (2008) and Scitable:
Hoopes, L. Genetic diagnosis: DNA microarrays and cancer, Nature
Education 1 (2008).
Read carefully for discussion: White et al., Microarray analysis of Drosophila
development during metamorphosis. Science 286:2179-2184 (1999). Bring to class half a page summarizing
White et al.'s findings about particular groups of genes and giving
examples of the genes in each group. Discussion
leader: Jocelyn Young
Thurs, Jan 29 No class: Review paper
topics posted
on Sakai, look for papers on PubMed, and use the time to make a tentative topic
choice for writing your term paper.
WEEK 3, Tues, Feb 3,
Discussion. 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,
Latchman p71, on neuron-specificity in RNA processing. Also read for
discussion, Celotto and Graveley,
Alternative splicing of the Drosophila Dscam Pre-mRNA is both temporally and
spatially regulated. Genetics 159:599-608
(2001). Bring to class half a page to a page summarizing the evidence used
by each of these authors and how it supports their hypotheses Discussion leader : Erik Lykken
Thurs, Feb 5, No Class. Day to continue 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 on
which your paper is based 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.
You may also mention a few findings from papers we do discuss if they provide
good background for your five 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 10. 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 half page 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).
Continue defining a paper topic and prepare to hand in materials due next
week by choosing a research paper (not a review article) you will 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. Sign up to lead discussions for the rest of the semester. Discussion leader: Alyssa Ward
Thurs, Feb
12, Discussion.
Continued post-transcriptional regulation. NonCoding RNA inhibition
of mRNA usage. Read
for background, on Scitable:
Phillips, T. Small non-coding RNA and gene
expression. Nature Education 1(1), (2008) and one of these two reviews: Fire,
AZ. Gene Silencing by
double-stranded RNA. (Nobel
lecture). Cell Death Diff 14 (12):
1998-2012 (2007) or Mello, CC,
Return to the RNAi World (Nobel Lecture).
Cell Death Diff 14 (12):
1023-2020 (2007). Let LH know if you
have trouble accessing these. 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: Kate Bayliss
WEEK 5: Tues, Feb 17, 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) and on Scitable, Ralston, A. & Brown, W. Chromatin
remodeling and DNase 1 sensitivity. Nature
Education 1(1), (2008).
Hoopes 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.
Thurs,
Feb 19, Discussion. NEW
TOPIC: Chromatin structure and epigenetic regulation; chromatin remodeling. Read Latchman commentary on section 5,
review article by Berger and Felsenfeld, Chromatin goes global, Molecular Cell 8:263-8 (2001), and Phillips, T. & Shaw, K. Chromatin
remodeling in eukaryotes. Nature
Education 1(1), (2008) on Scitable. 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); and Lee, W,
Tillo, D, Bray, N, Morse, R, Davis, R, Hughes, T, Nislow, C. A high-resolution atlas of
nucleosome occupancy in yeast. Nature Genetics 39:1235-1244 (Oct,
2007). Discussion leader: Sydney Freggiaro
WEEK 6: Tues, Feb 24.
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) and Mistelli, T., Chromosome
territories: The arrangement of chromosomes in the nucleus. Nature Education 1(1), (2008). 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: Amir Nabacht
Thurs, Feb 26, Discussion. Chromatin,
DNA methylation. Background: On Scitable read: Phillips, T. The role of methylation in gene
expression. Nature Education 1(1), (2008).
For discussion: McGhee and Ginder, p 125 in Latchman, on the role of DNA
methylation in regulation of chicken hemoglobin gene expression, and Kohyama,
J, Kojima, T, Takatsuka, E, Yamashita, T, Namiki, J, Hsieh, J, Gage, F,
Namihira, M, Okano, H, Sawamoto, K, and Nakashima, K. Epigenetic regulation of neural cell
differentiation plasticity in the adult mammalian brain. Proc
Natl Acad Sci, USA, 105:18012-18017 (2008).
Discussion leader:
Erik Lykken
WEEK 7: Tues, Mar 3, Discussion.
Chromatin, imprinting. Read for background on Scitable: Phillips, T. and Lobo, I. Genetic imprinting and X
inactivation. Nature Education 1(1), (2008) and Adams, J. Imprinting
and genetic disease: Angelman, Prader-Willi and Beckwith-Weidemann
syndromes. Nature Education 1(1), (2008). Read carefully
for discussion the articles 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) and 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: Ann Zhao
Thurs, Mar 5,
Discussion. Chromatin;
X-inactivation.
Read for introduction,
on Scitable, in the Chromosomes and Cytogenetics topic room, read this: Ahn, J. & Lee, J. X
chromosome: X inactivation. Nature
Education 1(1), (2008).
For discussion: Xu, N,
Donohoe, M, Silva, S, and Lee, Jeannie T. Evidence that homologous
X-chromosome pairing requires transcription and CTCF protein. Nature
Genetics 29(11):1390-1396 (2007) and Zhao,
J, Sun, BK, Erwin, JA, Song, JJ, and Lee, Jeannie T. Polycomb proteins targeted by a short repeat RNA to the mouse X
chromosome. Science 322:750-756 (2008).
Discussion leader: Alyssa Ward
WEEK 8: Tues, March 10,
Discussion. Chromatin: Histone acetylation and
methylation. Read for
background, Ralston, A. Examining
histone modifications with chromatin immunoprecipitation and quantitative
PCR. Nature Education 1(1), (2008) and Phillips, T. Regulation of
transcription and gene expression in eukaryotes. Nature Education 1(1) (2008). Read
carefully for discussion Kuo et al, Genes
Dev. 12:627-639 (1998), on action of the Gcn5 histone acetylase near an
active promoter, and Litt** et al.,
Correlation between histone lysine methylation and developmental changes at the
chicken beta globin locus. Science
293:2453-2455 (2001). Discussion leader: Amir Nobakht
Thurs, Mar 12. No class. LH at
Bioinformatics Institute at DOE/ASM. Use time to find the rest of your
articles for the paper and begin to analyze them.
WEEK OF MAR 16-20: Spring break, no
classes.
WEEK 9: Tues, March 24, 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. Lecture/Discussion leader: LH
Thurs, March 26. Discussion.
DNA Binding Sites: Promoters and Enhancers. For background, read Latchman
commentary 7, and
in the Nucleic Acids Structure and
Function room on Scitable, Clancy, S. DNA
transcription. Nature Education 1(1), (2008) and in the gene expression and regulation
room, Phillips, T. & Hoopes, L. Transcription
factors and transcriptional control in eukaryotic cells. Nature Education 1(1), (2008). For discussion read the Hanahan** paper, Latchman
p 173, on pancreatic tumorigenesis in transgenic mice caused by an enhancer
being attached to an oncogene. Discussion leader: Amir
Nobakht
WEEK
10. Tues, Mar 31. Discussion. Specific Transcription
Factors. Purification and
characterization. For background,
carefully read the Latchman
commentary on section 8, plus Ralston, A. Do transcription factors actually bind DNA? DNA
footprinting and gel shift assays. Nature
Education 1(1), (2008).
Read carefully for presentation both the Kadonaga and Tjian paper,
Latchman 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: Alyssa Ward
Thurs, Apr 2. Discussion,
Transcription factors, poising or stalling? RNA polymerase molecules can remain stuck at
the promoters of genes, not continuing to transcribe. This state has been called both poising and
stalling. Read for discussion these two
papers: Tamkun, JW, Stalled polymerases and transcriptional
regulation. Nature Genetics 39: 1421-22
(2007), 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: Jocelyn Young
Week 11, Tues Apr 7. Discussion. Cont: Transcription
factors: protein interaction. Read for
background, commentary for section 10 in Latchman.
Read for discussion Landschutz et al, p 237, on dimerization via the
leucine zipper structure, and Gonzalez and Montminy, Latchman p 257, on
control of the CREB transcription factor via phosphorylation controlled by cAMP
levels. Discussion leader: Syd
Freggairo
Paper Details, due Apr 20(Friday): 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 earlier) 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 9. Discussion, Transcription factors: regulatory signals
controlling transcription factors. 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: Kate
Bayliss
WEEK 12, Apr 14, 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: Jocelyn Young
Thursday, Apr 16: PAPER
IS DUE tomorrow, Friday by 5 PM. Discussion, Transcription factors in development. 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: Erik Lykken
WEEK 13, Tuesday, Apr 21, 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 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) 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: Syd Freggiaro
Thursday, Apr 23,
Retrospective on RNA Polymerase II (mRNA-specific RNA
polymerase) transcriptional regulation via transcription factors. 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? Also: planning discussion of the contenders for “Most Aesthetic Paper ” Discussion leader: Kate Bayliss
Week 14: Tuesday, April 28. Special topic as chosen by the class. TBA.
Discussion
leader:
Laura Hoopes
Thurs, Apr 30: Discussion. Discussion of papers
written by the students in the class, informal, with refreshments.
Tuesday,
May 5. 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!