IGP804: Genetic Systems
Fall 2004
Course Organizer: Neal Silverman, LRB 313, 6-5826
Co-organizer: Nick Rhind, LRB904, 6-8316
Kirsten Hagstrom, BiotechII-334, 6-6851
Michael Brodsky, LRB623, 6-1640
Victor Boyartchuk, LRB523, 6-4353
Ben Leung, LRB770J, 6-8542
Tuesdays, 9-11a.m., LRB 916
Syllabus
Week 1: September 7th
Screening for viable mutants:
Discussion leaders
Nick Rhind*
Kirsten Hagstrom
Hartwell LH. Mutants of Saccharomyces cerevisiae unresponsive to cell division
control by polypeptide mating hormone. J Cell Biol 1980, 85(3):811-22:
Ferguson EL, Sternberg PW, Horvitz HR. A genetic pathway for the specification
of the vulval cell lineages of Caenorhabditis elegans. Nature. 1987 Mar 1925;326(6110):259-67
Background/Additional reading
Jorgensen EM, Mango SE. The art and design of genetic screens:
Caenorhabditis elegans. Nat Rev Genet. 2002 May;3(5):356-69.
Herskowitz I. Life cycle of the budding yeast Saccharomyces cerevisiae.
Microbiol Rev. 1988 Dec;52(4):536-53.
Week 2: September 14th
Screening for lethal mutants
Discussion leaders
Neal Silverman
Mike Brodsky*
Nusslein-Volhard C, Wieschaus E. Mutations affecting segment number and
polarity in Drosophila. Nature. 1980 Oct 30;287(5785):795-801.
Tabata T, Eaton S, Kornberg TB. The Drosophila hedgehog gene is expressed
specifically in posterior compartment cells and is a target of engrailed regulation.
Genes Dev. 1992 Dec;6(12B):2635-45.
Background/Additional reading
Nobel lecture by Nusslein-Volhard
Nobel lecture by Weischaus
St. Johnston D. The Art and Design of Genetic Screens: Drosophila
melanogaster Nature Genetics Reviews, 2002, 3:176-188
Week 3: September 21st
Maternal Effect Mutations
Discussion leaders
Neal Silverman*
Kirsten Hagstrom
Anderson, Jurgens, Nusslein-Volhard, Establishment of dorsal-ventral polarity in
the Drosophila embryo: genetic studies on the role of the Toll gene product, Cell
1985, 42:779-89.
Kemphues KJ, Priess JR, Morton DG, Cheng NS, Identification of genes required
for cytoplasmic localization in early C. elegans embryos, Cell 1988, 52:311-20.
Background/Additional reading
Pellettieri J, Seydoux G, Anterior-posterior polarity in C. elegans and Drosophila-PARallels and differences. Science. 2002 Dec 6;298(5600):1946-50
Belvin MP, Anderson KV, A conserved signaling pathway: the Drosophila tolldorsal pathway. Annu Rev Cell Dev Biol. 1996;12:393-416.
Week 4: September 28th
Clonal Analysis
Discussion leaders
Mike Brodsky*
Ben Leung
Pagliarini RA, Xu T. A genetic screen in Drosophila for metastatic behavior.
Science. 2003 Nov 14;302(5648):1227-31.
Cui et al., Inducible and Reversible NR1 Knockout Reveals Crucial Role of the
NMDA Receptor in Preserving Remote Memories in the Brain. Neuron 41;78193, 2004
Background/Additional reading
St. Johnston D. The Art and Design of Genetic Screens: Drosophila
melanogaster Nature Genetics Reviews, 2002, 3:176-188
Chou and Perrimon, The autosomal FLP-DFS technique for generating germline
mosaics in Drosophila melanogaster. Genetics 1996, 144:1673-9
Sauer B, Inducible gene targeting in mice using the Cre/lox system. Methods
1998 14:381-92
Week 5: October 5th
Conditional Alleles
Discussion leaders
Nick Rhind*
Ben Leung
Novick P, Field C, Schekman R
Identification of 23 complementation groups required for post-translational events
in the yeast secretory pathway. Cell. 1980 Aug;21(1):205-15.
McGuire SE, Le PT, Osborn AJ, Matsumoto K, Davis RL. Spatiotemporal rescue
of memory dysfunction in Drosophila. Science. 2003 Dec 5;302(5651):1765-8.
Background/Additional reading
Schekman R, Novick P 23 genes, 23 years later. Cell. 2004 Jan 23;116(2
Suppl):S13-5St.
McGuire SE, Roman G, Davis RL. Gene expression systems in Drosophila: a
synthesis of time and space. Trends Genet. 2004 Aug;20(8):384-91.
Week 6: October 12th
Synthetics
Discussion leaders
Kirsten Hagstrom*
Neal Silverman
Mayer ML, Pot I, Chang M, Xu H, Aneliunas V, Kwok T, Newitt R, Aebersold R,
Boone C, Brown GW, Hieter P Identification of protein complexes required for
efficient sister chromatid cohesion. Mol Biol Cell. 2004 Apr;15(4):1736-45.
Ferguson EL, Horvitz HR. The multivulva phenotype of certain Caenorhabditis
elegans mutants results from defects in two functionally redundant pathways.
Genetics. 1989 Sep;123(1):109-21.
Background/Additional reading
Fay DS, Han M. The synthetic multivulval genes of C. elegans: functional
redundancy, Ras-antagonism, and cell fate determination. Genesis. 2000
Apr;26(4):279-84
Tong AHY et al. Systematic Genetic Analysis with Ordered Arrays of Yeast
Deletion Mutants. Science 2001 294:2364-68
Week 7: October 19th
Modifiers: Supression and Enhancements
Discussion leaders
Nick Rhind*
Mike Brodsky
Stevenson BJ, Rhodes N, Errede B, Sprague GF Jr. Constitutive mutants of the
protein kinase STE11 activate the yeast pheromone response pathway in the
absence of the G protein. Genes Dev. 1992 Jul;6(7):1293-304
Simon MA, Bowtell DD, Dodson GS, Laverty TR, Rubin GM Ras1 and a putative
guanine nucleotide exchange factor perform crucial steps in signaling by the
sevenless protein tyrosine kinase. Cell. 1991 Nov 15;67(4):701-16.
Background/Additional reading
Dohlman HG, Thorner JW. Regulation of G protein-initiated signal transduction
in yeast: paradigms and principles. Annu Rev Biochem. 2001;70:703-54.
St. Johnston D. The Art and Design of Genetic Screens: Drosophila
melanogaster Nature Genetics Reviews, 2002, 3:176-188
Week 8: October 26th – Topic/Hypothesis Due
Epistasis
Discussion leaders
Neal Silverman*
Nick Rhind
Hodgkin J Sex determination in the nematode C. elegans: analysis of tra-3
suppressors and characterization of fem genes. Genetics. 1986 Sep;114(1):1552
Novick, Ferro and Schekman, Order of events in the yeast secretory pathway.
Cell 25:461-69, 1981
Background/Additional reading
Hodgkin J. One lucky XX male: isolation of the first Caenorhabditis elegans sexdetermination mutants Genetics. 2002 Dec;162(4):1501-4.
Hansen D, Pilgrim D. Sex and the single worm: sex determination in the
nematode C. elegans. Mech Dev. 1999 May;83(1-2):3-15.
Schekman R, Novick P 23 genes, 23 years later. Cell. 2004 Jan 23;116(2
Suppl):S13-5St.
Week 9: November 2nd
RNAi
Discussion leaders
Kirsten Hagstrom*
Mike Brodsky
Murphy CT et al. Genes that act downstream of DAF-16 to influence the lifespan
of Caenorhabditis elegans. Nature. 2003 Jul 17;424(6946):277-83.
Berns et al. A large-scale RNAi screen in human cells identifies new
components of the p53 pathway. Nature. 2004 Mar 25;428(6981):431-7.
Background/Additional reading
Carpenter AE, Sabatini DM. Systematic genome-wide screens of gene function.
Nat Rev Genet. 2004 Jan;5(1):11-22.
News and View on Kenyon paper, Nature 2003.
Vousden and Lu, Live Or Let Die: The Cell’s Response to p53. Nature Reviews
Cancer 2002, 2:504-604.
November 9th
Retreat: No class
Week 10: November 16th – Abstract (including Specific Aims) Due
Cell Culture Genetics
Discussion leaders
Nick Rhind*
Victor Boyartchuk
Velazquez L, Fellous M, Stark GR, Pellegrini S. A protein tyrosine kinase in the
interferon alpha/beta signaling pathway. Cell. 1992 Jul 24;70(2):313-22.
Parada LF, Tabin CJ, Shih C, Weinberg RA. Human EJ bladder carcinoma
oncogene is homologue of Harvey sarcoma virus ras gene. Nature. 1982 Jun
10;297(5866):474-8.
Background/Additional reading
Chang EH, Furth ME, Scolnick EM, Lowy DR. Tumorigenic transformation of
mammalian cells induced by a normal human gene homologous to the oncogene
of Harvey murine sarcoma virus Nature. 1982 Jun 10;297(5866):479-83.
Pellegrini, John, Shearer, Kerr and Stark. Use of a Selectable Marker Regulated
by Alpha Interferon To Obtain Mutations in the Signaling Pathway. MCB 1989.
9:4605-12.
John J, McKendry R, Pellegrini S, Flavell D, Kerr IM, Stark GR. Isolation and
characterization of a new mutant human cell line unresponsive to alpha and beta
interferons. Mol Cell Biol. 1991 Aug;11(8):4189-95.
Shuai K, Liu B. Regulation of JAK-STAT signalling in the immune system.
Nature Rev Immunol. 2003 Nov;3(11):900-11.
H.R. Bourne, D.A. Sanders and F. McCormick, The GTPase superfamily: a
conserved switch for diverse cell functions. Nature 348 (1990), pp. 125–132.
Week 11: November 23rd
Sex Determination
Discussion leaders
Nick Rhind*
Kirsten Hagstrom
Cline T. Two closely linked mutations in Drosophila melanogaster that are lethal
to opposite sexes and interact with daughterless. Genetics 1978 90:684-698;
Page et al., The sex-determining region of the human Y chromosome encodes a
finger protein. Cell 1987 51:1091-1104.
AND
Palmer et al. Genetic evidence that ZFY is not the testis-determining factor.
Nature 1989 342:937-9,
Background/Additional reading
Graveley B. Sex, AGility, and the Regulation
of Alternative Splicing. Cell 2002, 109:409-412.
Canning CA and Lovell-Badge R. Sry and sex determination: how lazy can it
be? Trends in Genetics 2002, 18:111-113
Week 12: November 30th
Epigenetics
Discussion leaders
Nick Rhind*
Victor Boyartchuk
Pillus L, Rine J. Epigenetic inheritance of transcriptional states in S. cerevisiae.
Cell. 1989 Nov 17;59(4):637-47
Marisa S. Bartolomei, Sharon Zemel & Shirley M. Tilghman. Parental imprinting
of the mouse H19 gene Nature 1991 May 9;351(6322):153-5
Background/Additional reading
Susan M. Gasser and Moira M. Cockell, The molecular biology of the SIR
proteins. Gene 2001, 279: 1-16
Herskowitz, I. Life Cycle of the Budding Yeast Saccharomyces cerevisiae.
Microbiological Reviews 1988, 52:536-553.
Arney KL. H19 and Igf2--enhancing the confusion? Trends Genet. 2003
Jan;19(1):17-23.
Week 13: December 7th
Natural Variation and QTL Analysis
Discussion leaders
Victor Boyartchuk *
Neal Silverman
Kim UK, Jorgenson E, Coon H, Leppert M, Risch N, Drayna D. Positional cloning
of the human quantitative trait locus underlying taste sensitivity to
phenylthiocarbamide. Science. 2003 Feb 21;299(5610):1221-5
Dean, M., M. Carrington, C. Winkler, G.A. Huttley, M.W. Smith, R. Allikmets, J.J.
Goedert, S.P. Buchbinder, E. Vittinghoff, E. Gomperts, S. Donfield, D. Vlahov, R.
Kaslow, A. Saah, C. Rinaldo, R. Detels, and S.J. O'Brien, Genetic restriction of
HIV-1 infection and progression to AIDS by a deletion allele of the CKR5
structural gene. Hemophilia Growth and Development Study, Multicenter AIDS
Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort,
ALIVE Study. Science, 1996. 273(5283): p. 1856-62.
Background/Additional reading
Ron Korstanje & Beverly Paigen. From QTL to gene:
the harvest begins. Nature Genetics 31:235-36
Karl W. Broman. Review of statistical methods for QTL mapping in experimental
crosses. Lab Animal 30(7):44–52, 2001.
Week 14: December 14th -- Written Proposal Due.
Exceptions
Discussion leaders
Neal Silverman *
Nick Rhind
Stearns and Botstein. Unlinked noncomplementation: isolation of new conditionlethal Mutations in Each of the Tubulin genes.of Saccharomyces cerevisiae.
1988 Genetics 119:249-60.
Chen JL, Huisinga KL, Viering MM, Ou SA, Wu CT, Geyer PK. Enhancer action
in trans is permitted throughout the Drosophila genome. Proc Natl Acad Sci U S
A. 2002 Mar 19;99(6):3723-8.
Background/Additional reading
Duncan IW. Transvection effects in Drosophila. Annu Rev Genet. 2002;36:52156.
January 4th, 11th, and 18th
Oral Presentation of Proposals.
Proposal schedule:
October 26th-- Topic/Hypothesis due
November 16th-- Abstract (with Specific Aims) Due
December 14th-- Proposal Due
Late submissions will be docked a letter grade for each day past the deadline.
Student Proposal Format
Proposals can be in any area of genetics broadly defined, but cannot be on a
topic that your thesis/rotation lab studies. While any proposal with a genetic
theme is acceptable, it is strongly suggested that you propose experiments that
follow-up recent papers in genetics, including ones covered in class. While
preparing your proposal, you can assume that any gene (as defined by a preexisting mutation) can be rapidly identified and cloned. Proposals focused on
cloning are not acceptable. Additionally, you can assume that any gene (as
identified by non-genetic means) can be easily mutated, although you should
briefly describe how you would perform this. Furthermore, you can assume that
any antibody that you desire can be easily generated. In other words, for the
sake of this proposal, you can pretend that you live in an ideal world.
The written proposal is due December 14th and should be in the following format:
Abstract: ~ 1 page. Include hypothesis and specific aims.
Introduction: ~ 4 pages. Background information. Explain and justify
hypothesis.
Specific Aims: ~ 5 pages. Two or three aims. Each aim may include a
rationale (why perform this experiment), the proposed experiment(s), and
analysis of the experiment (expected results, interpretations, alternative
approaches). For each aim, you must explain how the experiments
proposed will address your hypothesis.
References
Maximum length: 10 pages, double-spaced (including figures, not including
references). Shorter proposal are fine. Proposals going over the page limit will
be docked one letter grade for every line over the limit.
Oral presentation of the proposals will begin January 4th.
Paper Discussions
Each student will present approximately 2 papers from the syllabus.
Presentations should include:
1. General background on the experimental system
2. Specific background to the assigned paper(s)
3. A hypothesis addressed in the paper
4. Description and critique of the experiments performed
5. Discussion of whether the experiments support/prove the hypothesis
EVERYONE should be prepared to discuss items 2 – 5.
Each class will be preceded by a short quiz to ensure that the papers are read.
Presentation should be limited to 45 minutes.
Grading
Grades will reflect:
1. participation in class discussions
50%
3 points per class: 1 point for answering the quiz question
1 point for speaking during class discussion
1 point for saying something intelligent.
2. paper presentations
25%
3. the proposal (written and oral)
25%