PCB5065 Advanced Genetics Fall 2007
Required Reading
& other useful interesting references
Required reading:
Discussion paper 1 (Thurs, Sept. 13)
Kimchi-Sarfaty, C et al. (2007) A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science 315:525
Komar, AA (2007) SNPs, silent but not invisible. Science 315:466
Parmley, JL & LD Hurst (2007) How do synonymous mutations affect fitness? BioEssays 29:515

Recommended reading:
Pearson H (2006) What is a gene? Nature 441:399
Benzer, S (1957) The elementary units of heredity, pp. 70-93 in: WD McElroy and B Glass (eds.)
A symposium on the chemical basis of heredity. The Johns Hopkins Press
Jacob, F and J Monod (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3:318

Other useful / interesting references for Dr. Hannah's section (not required):
Biemont, C and C Vieira (2006) Junk DNA as an evolutionary force. Nature 443:521 (a pan-species overview of transposons)
Holmes, FL (2006) RE: Reconceiving the Gene: Seymour Benzer's Adventures in Phage Genetics, Yale University Press
Avery L and S Waserman (1992) Ordering gene function: the interpretation of epistasis in regulatory hierarchies. Trends in Genetics 8:312
Walbot V and MMS Evans (2003) Unique features of the plant life cycle and their consequences. Nature Reviews Genetics 4:369

Required reading:
Discussion paper 2 (Tues, Oct 2)
Francis, KE, SY Lam, BD Harrison, AL Bey, LE Berchowitz and GP Copenhaver (2007) Pollen tetrad-based visual assay for meiotic recombination in Arabidopsis. Proc Natl Acad Sci USA 104:3913
Hawley, RS (2007) Meiosis in living color: fluorescence-based tetrad analysis in Arabidopsis. Proc Natl Acad Sci USA 104:3673

Required reading from Dr. Gabriel:
Bishop, D K and Zickler, D (2004) Early decision: Meiotic crossover interference prior to stable strand exchange and synapsis. Cell 117:9 
Kleckner, N (1996) Meiosis: How could it work? Proc Natl Acad Sci USA 93:8167
Muyrers, JPP et al. (2001) Techniques: recombinogenic engineering - new options for cloning and manipulating DNA.
Trends Biochem Sci 26:325
Orr-Weaver, TL & JW Szostak (1985) Double-strand-break repair model for recombination. Microbiol Rev 49:33
Stahl, FW (1994) The Holliday junction on its thirtieth anniversary. Genetics 138:241
Terasawa, M, Ogawa, H, Tsukamoto, Y, Shinohara, M, Shirahige, K, Kleckner, N, and Ogawa, T (2007) Meiotic recombination-related DNA synthesis and its implications for cross-over and non-cross-over recombinant formation. Proc Natl Acad Sci  USA 104:5965    

Other useful / interesting references for Dr. Gabriel's section (not required):
Dudas, A & M Chovanec (2004) DNA double-strand break repair by homologous recombination. Mutn Res 566:131
Johnson, RD and M Jasin (2000) Sister chromatid gene conversion is a prominent double strand break repair pathway in mammalian cells. EMBOJ 29:3398
Orr-Weaver, TL, JW Szostak & RJ Rothstein (1981) Yeast transformation: a model system for the study of recombination. Proc Natl Acad Sci USA 78:6354
Schiestl, RH & TD Petes (1991) Integration of DNA fragments by illegitimate recombination in S. cerevisiae. Proc Natl Acad Sci USA 88:7585
Joyce, EF and KS McKim (2007) When specialized sites are important for synapsis and the distribution of crossovers. BioEssays 29:217-226.    

Required reading:
Discussion paper 3 (Thurs, Oct 18)
Pollard et al. (2006) An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443:
Ponting & Lunter (2006) Human brain gene wins genome race. Nature 443:

Other useful/interesting references for Dr. Moore's section (not required):
Golubovsky & Manton (2005) Genome organization and three kinds of heritable changes. Frontiers in Bioscience 10:335
Petsko (2001) Size doesn't matter. Genome Biology 2:
Mattick (2003) Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. BioEssays 25:930
Schlotterer (2004) The evolution of molecular markers. Nature Rev Genet 5:63
Lamb et al. (2007) Plant chromosomes from end to end. Curr Opin Plant Biol 10:116
Kouzarides (2007) Chromatin modifications and their functions. Cell 128:693
Misteli (2007) Beyond the sequence: cellular organization of genome function. Cell 128:787
Cremer & Cremer (2001) Chromosome territories. Nature Rev Genet 2:292
Speicher & Carter (2005) The new cytogenetics: blurring the boundaries with molecular biology. Nature Rev Genet 6:782

Required reading:
Discussion paper 4 (Wed, Nov 7)
AJ Giraldez et al. (2006) Zebrafish MiR-430 promotes deadenlyation and clearance of maternal mRNAs. Science 312:75
SM Cohen and J Brennecke (2006) Mixed messages in early development. Science 312:65

Other useful/interesting references for Chase-McCarty section (not required):
Walbot&Evans (2003) Unique features of the plant life cycle and their consequences. Nature Rev Genet 4:369
Surani, AM (2007) Germ cells: the eternal link between generations. C R Biologies 330:474
Birky CW Jr (2001) The inheritance of genes in mitochondria and chloroplasts: Laws, mechanisms and models. Annual Review of Genetics 35:125
Taylor RW and DM Turnbull (2005) Mitochondrial mutations in human disease. Nature Reviews Genetics 6:389
Dent, RM, M Han and KK Niyogi (2001) Functional genomics of plant photosynthesis in the fast lane using Chlamydomonas reinhardtii. Trends in Plant Science 6:364
Bandi, C, AM Dunn, GDD Hurst and T Rigaud (2001) Inherited microorganisms, sex-specific virulence and reproductive parasitism. Trends in Parasitology 17:88
Harris, HL and HR Braig (2003) Sperm chromatin remodelling and Wolbachia-induced cytoplasmic incompatibility in Drosophila. Biochemical Cell Biology 81:229
Sinkins, SP & F Gould (2006) Gene drive systems for insect disease vectors. Nature Rev Genet 7:427
Pennisi, E (2003) Meiotic drive, bickering genes shape evolution. Science 301:1837
Kusano, A, C Staber, HYE Chan and B Ganetzky (2003) Closing the (Ran)GAP on segregation distortion in Drosophila. Bioessays 25:108
Chaudhury, AM and F Berger (2001) Maternal control of seed development. Cell & Developmental Biology 12:381
Christians, E (2003) Qland la mere est plus que responsable du devenir de sa progeniture. C R Medicine/Sciences 19:459
Cui&Kim (2007) Maternally derived transcripts. Reprod Fert Devel 19:25
Pennisi (2001) Behind the scenes of gene expression. Science 293:1064-1067
Riddihough G and E Pennisi (2001) The evolution of epigenetics. Science 293:1063
Goldberg, AD, CD Allis & E Bernstein (2007) Epigenetics: A landscape takes shape. Cell 128:635
Walter, J and M. Paulsen (2003) Imprinting and Disease. Seminars in Cell and Developmental Biology 14:101
Scott RJ and M Spielman (2006) Deeper into the maize: new insights into genomic imprinting in plants. BioEssays 28:1167
Edwards, CA & AC Ferguson-Smith (2007) Mechanisms regulating imprinted genes in clusters. Curr Opin Cell Biol 19:281
Chandler, VL (2007) Paramutation: from maize to mice. Cell 128:641
Mello, CC and D Conte, Jr (2004) Revealing the world of RNA interference. Nature 431:338
Gendrel, A-V and V Colot (2005) Arabidopsis epigenetics: when RNA meets chromatin. Current Opinion in Plant Biology 8:142
Chu, C-Y and TM Rana (2007) Small RNAs: regulators and guardians of the genome. J Cell Physiol 213:412
Ambrose, KV and PW Ingham (2003) The transformation of the model organism: a decade of developmental genetics. Nature Genetics Supplement 33:285
Pick, L (1998) Segmentation: painting stripes from flies to vertebrates. Dev Gent 23:1
Lemons, D and W McGinnis (2006) Genomic evolution of hox gene clusters. Science 313:1918

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