1. Sujuan Ye, Alexander M. Erkine, and Yunkai Liu Department of Computer Science University of South Dakota

2.  Induced when a cell undergoes various types of environmental stresses like heat, cold and oxygen deprivation.  Present in all organisms - from bacteria to human.  Provide thermo-tolerance to cells exposed to heat stress.  Protect organisms against stress-induced damage.  Act as chaperones, which bind and stabilize proteins, aid protein folding.  Target proteins for degradation. (e.g. HSP60, HSP70, HSP100)

3.  Heat shock transcription factor (HSF), which binds to the heat shock elements (HSE) ◦ Perfect(PFT):TTCnnGAAnnTTC ◦ GAP(GAP): TTCn-{5bp}-nTTCnnGAA ◦ STEP(STP): GAAn-{5bp}-nGAAn-{5bp}-nGAA  Msn2 and Msn4 transcription factors, which bind to the stress response element (STRE). ◦ AGGGG-{1~100bp}-AGGGG

4. HSE STRE PFTGAPSTPSTRE Expected density (per kb) 0.023540.024580.032710.04813 Density of HSGs 0.138140.096100.114110.30330 Ratio5.86783.90903.48896.3024

5. Number of genesGene examples HSF/HSE310 HSP60, HSP31,HSP10, HSC82, UBI4, SSA3, EDC2 MSN2/MSN4/STRE (or HSE(non- consensus)+STRE) 297 DDR2, HSP26, HSP12, CTT1, TPS2, PGM2 HSE+STRE25 HSP78, HSP104, HSP42, SSA1, HRK1, MDJ1

6.  Some Hsf1-regulated genes lack HSE in the promoter region  Intergenic transcripts could regulate the transcription of adjacent gene by transcription interference. -600 -2000 GAACATTCTCGAA TATAAA -1523 -1438 GLE2 TATATA -161 -600 -2000 TTCAGGAAGCTTCTATAAA DAK2 -1551 -1531 -107 TATATA