BICH/GENE 631, Spring 2007

READING LIST

 

Jan. 18 – Hunting for mutants in yeast

1. Mutants of yeast defective in sucrose utilization (1981) Carlson, M, Osmond, B, and Botstein, D. Genetics 98:25-40.

 

Hu chapter 1

Hu chapter 2

 

Jan. 23 – Hunting for mutants in a vertebrate model system

2. Large-scale mutagenesis in the zebrafish: in search of genes controlling development in a vertebrate (1994) Mullins, MC, Hammerschmidt, M, Haffter, P, and Nusslein-Volhard, C. Current Biology 4:189-202.

 

Hu chapter 3

 

Jan. 25 – Isolation of mutations – selections vs. screens

3. Use of the HPRT gene and the HAT selection technique in DNA-mediated transformation of mammalian cells: first steps toward developing hybridoma techniques and gene therapy (1992) Szybalski, W. Bioessays 14:495-500.

 

Hu chapter 4

 

Jan. 30 – Cloning by complementation

4. Cloning by function: an alternative approach for identifying yeast homologs of genes from other organisms (1990) Kranz, JE and Holm, C. Proc. Natl. Acad. Sci. USA 87:6629-6633.

 

Hu chapter 5

 

Feb. 6 – Targeted homologous recombination

5. Gene targeting in the mouse (1994) Melton, DW. Bioessays 16:633-638.

 

Hu chapter 6

Hu chapter 7

Hu chapter 8

 

6. Gene targeting: things go better with Cre (1997) Jiang, R, and Gridley, T. Current Biol. 7:R321-R323.

 

Feb. 8 – Transposon mutagenesis

7. Starting a new genetic system: lessons from Bacteroides (2000) Salyers, AA, Boheyo, G, and Shoemaker, NB. Methods 20:35-46.

 

Feb. 13 – Suppression and synthetics

8. A suppressor of SNF1 mutations causes constitutive high-level invertase synthesis in yeast (1984) Carlson, M, Osmond, BC, Neigeborn, L, and Botstein, D. Genetics 107:19-32.

 

Hu chapter 9

 

Feb. 15 – Genetic analysis of signal transduction pathways

9. A genetic study of signaling processes for repression of PHO5 transcription in Saccharomyces cerevisiae (1998) Lau, WW, Schneider, KR, and O’Shea, EK. Genetics 150:1349-1359.

 

Feb. 20 – Pathway analysis from biosynthetic to developmental

10. A genetic method for determining the order of events in a biological pathway (1973) Jarvik, J, and Botstein, D. Proc. Natl. Acad. Sci. USA 70:2046-2050.

 

Feb. 22 – Chromatin and transcription; transcription factor modularity

11. Chromatin as an essential part of the transcriptional mechanism (1992) Felsenfeld, G. Nature 355:219-224.

 

12. Transcriptional activation by recruitment (1997) Ptashne, M, and Gann, A. Nature 386:569-577.

 

Feb. 27 – Transcriptional synergy

13. Modulation of promoter occupancy by cooperative DNA binding and activation-domain function is a major determinant of transcriptional regulation by activators in vivo (1996) Tanaka, M. Proc. Natl. Acad. Sci. USA 93:4311-4315.

 

March 1 – Mechanisms of transcriptional synergy

14. Multiple TAFIIs directing synergistic activation of transcription (1995) Sauer, F, Hansen, SK, and Tjian, R. Science 270:1783-1788.

 

March 6 – ATP-dependent chromatin remodeling; histone modification

15. Eukaryotic transcription: an interlaced network of transcription factors and chromatin-modifying machines (1998) Kadonaga, JT. Cell 92:307-313.

 

16. Translating the histone code (2001) Jenuwein, T, and Allis, CD. Science 293:1074-1080.

 

March 8 – Recruitment to promoters

17. Modifying gene expression by altering core promoter chromatin architecture (2002) Lomvardas, S, and Thanos, D. Cell 110:261-271.

 

Review article. Ordered Recruitment: Gene-Specific Mechanism of Transcription Activation (2002) Cosma, MP. Mol. Cell 10:227-236.

 

March 20 – DNA methylation and histone deacetylation

18. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex (1998) Nan, X, Ng, HH, Johnson, CA, Laherty, CD, Turner, BM, Eisenman, RN, and Bird, A. Nature 393:386-389.

 

March 22 – Action at a distance – looping mechanisms for enhancer function

19. Action at a distance along a DNA (1988) Wang, JC, and Giaever, GN. Science 24:300-304.

 

March 27 – Action at a distance – sliding mechanisms for enhancer function

20. A transcriptional enhancer whose function imposes a requirement that proteins track along DNA (1992) Herendeen, DR, Kassavetis, GA, and Geiduschek, EP. Science 256:1298-1303.

 

March 29 – A network of protein-protein interactions regulate RNA splicing

21. New components of the spliced leader RNP required for nematode trans-splicing (2002) Denker, JA, Zuckerman, DM, Maroney, and PA, Nilsen, TW. Nature 417:667-670.

 

April 3 – Control  of mRNA stability by recruitment of the “exosome”

22. AU binding proteins recruit the exosome to degrade ARE-containing mRNAs (2001) Chen, CY, Gherzi, R, Ong, SE, Chan, EL, Raijmakers, R, Pruijn, GJ, Stoecklin, G, Moroni, C, Mann, M, and Karin, M. Cell 107:451-464.

 

April 5 – Expansion of the genetic code via RNA editing

23. Separate insertion and deletion subcomplexes of the Trypanosoma brucei RNA editing complex (2003) Schnaufer, A, Ernst, NL, Palazzo, SS, O’Rear, J, Salavati, R, and Stuart, K. Mol. Cell 12:307-319.

 

April 10 – Cell-fate determination by localized gene regulation in early Drosophila embryos

24. Bicoid associates with the 5’-cap-bound complex of caudal mRNA and represses translation (2002) Niessing, D, Blanke, S, and Jackle, H. Genes Dev. 16:2576-2582.

 

April 12 – Regulation of translation by “tiny” RNAs

25. A microRNA in a multiple-turnover RNAi enzyme complex (2002) Hutvagner, G, and Zamore, PD. Science 297:2056-2060.

 

April 17 – Regulation of telomere length

26. Nucleolar protein PinX1p regulates telomerase by sequestering its protein catalytic subunit in an inactive complex lacking telomerase RNA (2004) Lin, J, and Blackburn, EH. Genes Dev. 18:387-396.

 

April 19 – Co-transcriptional maturation of mRNA

27. Cotranscriptional spliceosome assembly dynamics and the role of U1 snRNA:5’ss base pairing in yeast (2005) Lacadie, SA, and Rosbash, M. Mol. Cell 19:65-75.

 

April 24 –

 

April 26 –