Syllabus for Biology 164

Seminar Syllabus for Biology 164: Genetic Regulation in Eukaryotes, 2004. (Refer to laboratory section of web pages for laboratory schedule)

Required text: Latchman, D. S. Editor, Landmarks in Gene Regulation (collection of papers with commentary) Portland Press, London/Miami, 1997. Also, you will need to obtain and review copies of the more current assigned papers below. Generally pdfs can be obtained from the library web site. If at all possible, look at the figures in color, if they are given in color. Otherwise, you will not be able to interpret and evaluate the data presented. If you have a problem getting a pdf, let me know and I will negotiate with the library for us.

Optional speaking/writing intensive students: please let Dr. Hoopes know you want to get speaking and/or writing intensive credit after the first class, since you will need to complete additional assignments to receive this credit and these need to be arranged between you and LH.

WEEK 1: Tues, August 31 , Lecture/Discussion. Eukaryotic regulation overview (evidence that messenger RNA rather than DNA provides the basis for tissue specific regulation). Optional reading in background text Genes VII, pp 80-81(gene expression), chapter 5 (mRNA), 234-240 (transcription). Differences between prokaryotic and eukaryotic regulation: role of eukaryotic chromatin structure. Background readings: K Struhl, Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 98:1-4 (1999); Martens, J and Winston, F. Recent advances in understanding chromatin remodeling by Swi/Snf complexes. Current Opinion in Genetics and Development 13:136-142 (2003). Discussion led by Hoopes.
Sign up to lead discussions for session in second week and first session in third week.

Thurs Sept 2. Discussion. Topic: Regulation of mRNA Concentrations. 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 of approximately 1/2 page length summarizing White et al.'s findings about particular groups of genes and giving examples of the genes in each group. Be sure to explain the difference between seeing the level of a particular mRNA change and induction/repression of a gene (hint: what kind of processes besides increased or decreased gene activity might affect the level of the mRNA?) Discussion leader: Julia Maxson

WEEK 2: Tues Sept 7. Discussion. Topic: Post-transcriptional regulation by alternative splicing of precursor RNAs. Read section 3 in Latchman. Read carefully for discussion Crenshaw, p71, on neuron-specificity in RNA processing. Bring to class a half-page long paragraph summarizing the evidence used by these authors and how it supports their hypothesis.
Sign up to lead discussions for rest of semester. Brief discussion of scientific aesthetics: early collection of our ideas about what makes a paper 'beautiful'.
Discussion leader: Kendra Lipinski

Thurs, September 9. Special event: visit of Sarah Elgin, Washington Univ, St. Louis, and Pomona Alumna. She will deliver a lecture from 11-12 following our class, and you are strongly encouraged to attend. Discussion of Chromatin Organization. Review Struhl paper and Martens/Winston paper. Read for background discussion: Read carefully for discussion and as background for lecture:

Elgin, S.C.R., and S.I.S. Grewal (2003) "Primer. Heterochromatin: Silence is Golden," Curr. Biol. 13, R895-R898.

Pal-Bhadra, M., B. A. Leibovitch, S. G. Gandhi, M. Rao, U. Bhadra, J. A. Birchler, S. C. R. Elgin (2004) "Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery," Science 303, 669-672.

WEEK 3, Tues, Sept 14, Discussion. 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 1/2 page long paragraph summarizing the difference between the mechanism described in this paper and that in the Casey et al. paper (which was not 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 are given below the detailed syllabus and at a separate site under the course web page. See a brief description of the paper you will be writing below, under Sept 21 and longer descriptions under Nov 16 and Nov 23.
Discussion leader: Kyle Lancaster

Thurs, Sept 16, Discussion. RNAi inhibition of mRNA usage. Read carefully for discussion these papers: 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) and Chen, C-Z, Li, L, Lodish, H, and Bartel, D. MicroRNAs modulate hematopoietic lineage differentiation. Science 303:83-86 (2004) Discussion leader: Ganesh Davendra

Brief discussion with LH on making sure your article for Tuesday's assignment re the course paper is not a review article.

WEEK 4: Tues, Sept 21, Topic retrospective: regulation of gene expression via transcription and post-transcriptional regulation, group discussion leader LH. 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 ALL BIBLIOGRAPHIC DETAILS (authors, complete title, journal, volume, pages, year) ON ONE ARTICLE FOR YOUR PAPER (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. Optional Genes VII reading: Chapter 19 (nucleosomes and packing of chromatin). LH will lead discussion. Review Struhl, Martens and Winston, Elgin and Grewal from previous discussions.

Thurs, Sept 23, Discussion. 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) and Bochar et al., BRCA1 is associated with a human SWI/SNF-related complex: linking chromatin remodeling to breast cancer. Cell 102:257-265 (2000).
Discussion leader: Liz Groothuis

WEEK 5: Tues, Sept 28, Discussion. Chromatin structure and epigenetic regulation, nuclear matrix interactions. Read carefully for discussion 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: Jennifer Hardee

Thurs, Sept 30, 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) 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 and Amedeo et al., Disruption of the plant gene MOM releases transcriptional silencing of methylated genes. Nature 405:203-208 (2000). Discussion leader: Braden Boice

WEEK 6: Tues, Oct 5, Discussion. Chromatin, imprinting. Read for background Allshire and Bickmore, Pausing for thought on the boundaries of imprinting. Cell 102:705-708 (2000.) 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). Also read Bourc'his et al., Dnmt3L and the establishment of maternal genomic imprints. Science 294:2536-2539 (2001).
Discussion leader: Amelia Huck

Thurs, Oct 7, Discussion. Chromatin; X-inactivation. Read for both introduction and for discussion: Panning et al., X chromosome inactivation is mediated by Xist RNA stabilization. Cell 5:907-916. Read for discussion only: Okamoto, I, Otte, A, Allis, C D, Reinberg, D, and Heard, E. Epigenetic dynamics of imprinted X Inactivation during Early Mouse Development. Science303:644-649 (2004).
Discussion leader: Paul Haines

WEEK 7: Tues, Oct 12, Discussion. Chromatin: Histone acetylation and methylation. Reread Struhl for background. Read carefully for discussion Kuo et al, Genes Dev. 12:627-639 (1999), 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 b-globin locus. Science 293:2453-2455 (2001).
Discussion leader: Lisa Park (presentation for Speaking Intensive)

Thurs, Oct 14, Topic retrospective: chromatin and epigenetic regulation, Bring to class a paragraph answering these questions: For this 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? Group discussion leader LH. Also,
Short Lecture/discussion on new topic: DNA Binding Sites for Regulatory Proteins: Promoters and enhancers. Optional reading in Genes VII p618-640 (Initiation of transcription; promoters and enhancers). LH.

WEEK 8: Tues, Oct 19, Fall Break, no class.

Thurs, Oct 21, Discussion. DNA Binding Sites: Promoters and Enhancers. Read Latchman commentary 7; read carefully for discussion Banerji et al., p 161, on an enhancer that regulates expression of antibody genes and an early paper on the ChIP on Chip technique: Iyer et al, Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409:533-538 (2001); see: http://genome-www.stanford.edu/chromatinip/sbfmdf.pdf .
Discussion leader: Rich Cannon

WEEK 9: Tues, Oct 26. No Class, LH at HHMI grant program directors' meeting in DC.

Thurs, Oct 28, Discussion, DNA binding sites. Review Latchman commentary 7. Read carefully for discussion the Hanahan paper, p 173, on pancreatic tumorigenesis in transgenic mice caused by an enhancer being attached to an oncogene.
Discussion leaders: Kendra Lipinski and Braden Boice

WEEK 10. Tues, Nov 2, Lecture/Discussion RNA Polymerase II; general and specific transcription factors. Optional reading in Genes VII pp641-646. Read as background Cramer et al., Structural basis of transcription: RNA polymerase II at 2.8 Angstrom resolution. Science 292:1863-1882 (2001). LH leads discussion.

Thurs, Nov 4, Discussion. For background, carefully read the Latchman commentary on section 8. 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 leaders: Amelia Huck and Richard Cannon

WEEK 10. Tues, Nov 9, Discussion, Transcription factors (general). Read the reviews, Goodrich et al, Contacts in Context: Promoter specificity and macromolecular interactions in transcription. Cell 84:825-830 (1996) and Cramer et al. Structural basis of transcription: RNA polymerase II at 2.8 Angstrom Resolution, Science 292:1863-1882 (2001.) Read carefully for discussion Li et al., Distinct classes of yeast promoters revealed by differential TAF recruitment, Science 288:1242-1244 (2000). Discussion leaders: Kyle Lancaster and Paul Haines
Thurs, Nov 11, Discussion, Transcription factors. Skim the article by Kissinger et al, p 223, on the crystal structure 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). Discussion Leader: Liz Groothuis (could add a helper)

WEEK 11, Tues, Nov 16, Discussion, Transcription factors. Read the commentary for section 10 in Latchman. Read carefully 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, which is in turn controlled by cAMP levels . Discussion leader: Jennifer Hardee (could add a helper)
NOTE: Paper is due next Tuesday, the Tuesday before Thanksgiving!! 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 it Sept 21) 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. 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.

Thursday, Nov 18, Discussion, Transcription factors. Read 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 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). . Discussion leader: Lisa Park (presentation for Speaking Intensive)

WEEK 12, Tuesday, Nov 23: PAPER IS DUE IN CLASS TODAY!! 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 from the recent literature on an approved topic. The paper should highlight the relationship of the area chosen to other topics covered in the course, should examine the logic of the experiments done by each team and the support they provide for the hypotheses, and should discuss the relationship between the findings in the various papers. If appropriate, you should include your model of how the regulatory system under study appear to work. Complete and accurate bibliographic information should be presented in the style used by the journal Molecular and Cellular Biology. Discussion, Transcription factor regulation. Read for discussion Martinez-Garcia et al., Direct targeting of light signals to a promoter element-bound transcription factor. Science 288:859-891 (2000), and Tran, H, Brunet, A, Grenier, J, Datta, S, Fornace, A, DiStefano, P, Chiange, L, and Greenberg, M. DNA repair pathway stimulated by the forkhead transcription factor FOX03a through the Gadd45 protein. (related to life span regulation) Science 296:530-534 (2002). Discussion leader: Hoopes

Thursday, November 25, Thanskgiving, no class! Enjoy feasting and resting!

WEEK 13, Tuesday, Nov 30, 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 leaders: Julia Maxson and Ganesh Davendra

Thursday, December 2, 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 lass class discussion of the contenders for aesthetic paper of the year.

Week 14: Tuesday, December 7, last day of class, Discussion. MANDATORY CLASS!! If you must miss this class, you must make prior arrangements with Dr. Hoopes. 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!).

NO FINAL EXAMINATION, HAVE A GREAT BREAK!