A Genomic Survey of Heat Shock Transcription Factor Binding Sites in Saccharomyces cerevisiae
description
Transcript of A Genomic Survey of Heat Shock Transcription Factor Binding Sites in Saccharomyces cerevisiae
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