Reading

Project essentials

• Caroline M. Ajo-Franklin et al. Rational design of memory in eukaryotic cells. (2007) PMID 17875664
• Attila Becskei et al. Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. (2001) PMID 11350942
• Christina B. Tyson et al. Dependency of size of Saccharomyces cerevisiae cells on growth rate. (1978) PMID 374379
• Nathan C. Shaner et al. A guide to choosing fluorescent proteins. (2005) PMID 16299475

Transcriptional/translational control

• Gudrun Bjornsdottir and Lawrence C. Myers. Minimal components of the RNA polymerase II transcription apparatus determine the consensus TATA box. (2008) PMID 18385157
• Thomas Masek et al. Hepatitis C virus internal ribosome entry site initiates protein synthesis at the authentic initiation codon in yeast. (2007) PMID 17554033
• Wei Zhouet et al. Isolation and identification of short nucleotide sequences that affect translation initiation in Saccharomyces cerevisiae. (2002) PMID 12679518

Eukaryotic activation/repression domains

• Gerald Thiel et al. How mammalian transcriptional repressors work. (2004) PMID 15233782
• Gemma Bellí et al. An activator/repressor dual system allows tight tetracycline-regulated gene expression in budding yeast. (1998) PMID 9461451
• Jae-Ryeon Ryu et al. Cell-type specificity of short-range transcriptional repressors. (2001) PMID 11687630
• Tania M. Malavé and Sharon Y.R. Dent. Transcriptional repression by Tup1-Ssn6. (2006) PMID 16936817

Prokaryotic DNA binding domains (+ affinity mutations)

• M. Madan Babu and Sarah A. Teichmann. Functional determinants of transcription factors in Escherichia coli: protein families and binding sites. (2003) PMID 12547514
• Christian Berens and Wolfgang Hillen. Gene regulation by tetracyclines. Constraints of resistance regulation in bacteria shape TetR for application in eukaryotes. (2003) PMID 12869186
• A. Wissmann et al. Amino acids determining operator binding specificity in the helix-turn-helix motif of Tn10 Tet repressor. (1991) PMID 1756721
• Hillary C.M. Nelson and Robert T. Sauer. Lambda repressor mutations that increase the affinity and specificity of operator binding. (1985) PMID 3161621
• Nicholas Benson et al. Mutant lambda repressors with increased operator affinities reveal new, specific protein-DNA contacts. (1992) PMID 1531047
• P. Oertel-Buchheit et al. Isolation and characterization of LexA mutant repressors with enhanced DNA binding affinity. (1992) PMID 1602473
• Liskin Swint-Kruse et al. Perturbation from a distance: mutations that alter LacI function through long-range effects. (2003) PMID 14636069

Protein degradation motifs

• Emily R. Hildebrandt and M. Andrew Hoyt. Cell cycle-dependent degradation of the Saccharomyces cerevisiae spindle motor Cin8p requires APC(Cdh1) and a bipartite destruction sequence. (2001) PMID 11694576
• Janet L. Burton and Mark Solomon. D box and KEN box motifs in budding yeast Hsl1p are required for APC-mediated degradation and direct binding to Cdc20p and Cdh1p. (2001) PMID 11562348
• Sofie R. Salama et al. G1 cyclin degradation: the PEST motif of yeast Cln2 is necessary, but not sufficient, for rapid protein turnover. (1994) PMID 7969135
• Carolina Mateus and Simon V. Avery. Destabilized green fluorescent protein for monitoring dynamic changes in yeast gene expression with flow cytometry. (2000) PMID 11015728
• Catherine Berset et al. Transferable domain in the G(1) cyclin Cln2 sufficient to switch degradation of Sic1 from the E3 ubiquitin ligase SCF(Cdc4) to SCF(Grr1). (2002) PMID 12052857
• Matthew D. Petroski and Raymond J. Deshaies. Redundant degrons ensure the rapid destruction of Sic1 at the G1/S transition of the budding yeast cell cycle. (2003) PMID 12963827
• Alexander Varshavsky. The N-end rule: functions, mysteries, uses. (1996) PMID 8901547

Nuclear localistation

• Gabriel Schlenstedt et al. Reconstitution of nuclear protein transport with semi-intact yeast cells. (1993) PMID 8227140
• Julia M. Sidorova et al. Cell cycle-regulated phosphorylation of Swi6 controls its nuclear localization. (1995) PMID 8590795
• Michelle T. Harreman et al. Regulation of nuclear import by phosphorylation adjacent to nuclear localization signals. (2004) PMID 14998990

Site-specific proteases

• Sung Yun Kim et al. In vivo determination of substrate specificity of hepatitis C virus NS3 protease: genetic assay for site-specific proteolysis. (2000) PMID 10933854
• Hara Kang et al. An improved strategy for a genetic assay for site-specific proteolysis. (2001) PMID 11355710
• Sung Yun Kim et al. Detection of site-specific proteolysis in secretory pathways. (2002) PMID 12163035

mRNA instability

• T. Chinnappan Santiago et al. The relationship between mRNA stability and length in Saccharomyces cerevisiae. (1986) PMID 3537957
• Reut Shalgi et al. A catalog of stability-associated sequence elements in 3'UTRs of yeast mRNAs. (2005) PMID 16207357
• Tina Gill et al. RNase MRP cleaves the CLB2 mRNA to promote cell cycle progression: novel method of mRNA degradation. (2003) PMID 14729943
• Bernard J. de la Cruz et al. The role of the 5' untranslated region (UTR) in glucose-dependent mRNA decay. (2002) PMID 12112242
• Benoit Pierrat et al. The 5' untranslated region of the PPR1 regulatory gene dictates rapid mRNA decay in yeast. (1993) PMID 8370540

Toggle switches

• Timothy S. Gardner et al. Construction of a genetic toggle switch in Escherichia coli. (2000) PMID 10659857
• Beat P. Kramer and Martin Fussenegger. Hysteresis in a synthetic mammalian gene network. (2005) PMID 15972812

BioBrick assembly

• Tom Knight. Idempotent Vector Design for Standard Assembly of Biobricks (2003) [http://web.mit.edu/synbio/release/docs/biobricks.pdf]
• Ira E. Phillips and Pamela A. Silver. A New Biobrick Assembly Strategy Designed for Facile Protein Engineering (2006) [http://dspace.mit.edu/bitstream/handle/1721.1/32535/PhillipsSilverFusion.pdf?sequence=1]

Miscellaneous

• Pawan K. Dhar. The next step in biology: a periodic table? (2007) PMID 17914242