Transcript A Genomic Survey of Heat Shock Transcription Factor Binding Sites

Sujuan Ye, Alexander M. Erkine, and Yunkai Liu
Department 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
HSE
Density(100bp)
0.8
STRE
0.35
0.7
0.3
0.6
0.25
0.5
0.2
0.4
0.3
0.15
0.2
0.1
0.1
0.05
0
-1000
-800
-600
-400
-200
PFT
0
0
-1000
GAP
-800
-600
STP
-400
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
-200
0
Number of genes
Gene examples
HSF/HSE
310
HSP60, HSP31,HSP10,
HSC82, UBI4, SSA3, EDC2
MSN2/MSN4/STRE
(or HSE(nonconsensus)+STRE)
297
DDR2, HSP26, HSP12,
CTT1, TPS2, PGM2
HSE+STRE
25
HSP78, 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.
GAACATTCTCGAA
-2000
-1523
TTCAGGAAGCTTC
-2000
-1551
TATAAA
-1438
TATATA
-600
TATAAA
-1531
-161
TATATA
-600
GLE2
-107
DAK2