Sujuan Ye, Alexander M. Erkine, and Yunkai LiuDepartment of Computer Science

University of South Dakota

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)

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

HSESTRE

PFT GAP STP STRE

Expected density(per kb)

0.02354 0.02458 0.03271 0.04813

Density of HSGs

0.13814 0.09610 0.11411 0.30330

Ratio 5.8678 3.9090 3.4889 6.3024

Number of genes Gene examples

HSF/HSE 310HSP60, HSP31,HSP10,

HSC82, UBI4, SSA3, EDC2

MSN2/MSN4/STRE(or HSE(non-

consensus)+STRE)297

DDR2, HSP26, HSP12, CTT1, TPS2, PGM2

HSE+STRE 25HSP78, HSP104, HSP42,

SSA1, HRK1, MDJ1

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

GLE2TATATA

-161

-600-2000

TTCAGGAAGCTTC TATAAA DAK2

-1551 -1531 -107

TATATA