binding site cooperativity and dual signal integration in cap1a1 induction
TRANSCRIPT
![Page 1: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/1.jpg)
Pascal Schulthess, Albert Braeuning, Alexandra Löffler, Michael Schwarz, and Nils Blüthgen
Binding Site Cooperativity and Dual Signal Integration in CYP1A1 Induction
1
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CYP1A expression in liver
2Braeuning, A. & Schwarz, M. Biol. Chem. 391, 139–148 (2010)
rela
tive
mR
NA
exp
ress
ion [a
. u.]
0
3
6
9
100
150
200
250
300
TCDD – +
CYP1A1primary mousehepatocytes
n=5
Braeuning, A., Köhle, C., Buchmann, A. & Schwarz, M. Toxicol. Sci. 122, 16–25 (2011).
![Page 3: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/3.jpg)
CYP1A expression in liver
WT
CYP1A
P
C
2Braeuning, A. & Schwarz, M. Biol. Chem. 391, 139–148 (2010)
rela
tive
mR
NA
exp
ress
ion [a
. u.]
0
3
6
9
100
150
200
250
300
TCDD – +
CYP1A1primary mousehepatocytes
n=5
Braeuning, A., Köhle, C., Buchmann, A. & Schwarz, M. Toxicol. Sci. 122, 16–25 (2011).
![Page 4: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/4.jpg)
CYP1A expression in liver
WT
CYP1A
P
C
ß-ca
t k.o
.
P
C
2Braeuning, A. & Schwarz, M. Biol. Chem. 391, 139–148 (2010)
rela
tive
mR
NA
exp
ress
ion [a
. u.]
0
3
6
9
100
150
200
250
300
TCDD – +
CYP1A1primary mousehepatocytes
n=5
Braeuning, A., Köhle, C., Buchmann, A. & Schwarz, M. Toxicol. Sci. 122, 16–25 (2011).
![Page 5: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/5.jpg)
Wnt
TCDD
AhR
Arnt
Lrp5/6Fzd
b-cat
AhR and ß-catenin converge on CYP1A1 promoter
3
TCFCYP1A1
DREDREDRE DRE RNAP
![Page 6: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/6.jpg)
Wnt
TCDD
AhR
Arnt
Lrp5/6Fzd
b-cat
AhR and ß-catenin converge on CYP1A1 promoter
3
TCFCYP1A1
DREDREDRE DRE RNAP
TCFCYP1A1
DREDREDRE DRE RNAP
![Page 7: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/7.jpg)
Wnt
TCDD
AhR
Arnt
Lrp5/6Fzd
b-cat
AhR and ß-catenin converge on CYP1A1 promoter
3
TCFCYP1A1
DREDREDRE DRE RNAP
TCFCYP1A1
DREDREDRE DRE RNAP
How do DREs cooperate?
![Page 8: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/8.jpg)
Wnt
TCDD
AhR
Arnt
Lrp5/6Fzd
b-cat
AhR and ß-catenin converge on CYP1A1 promoter
3
TCFCYP1A1
DREDREDRE DRE RNAP
TCFCYP1A1
DREDREDRE DRE RNAP
How are 2 signals integrated?
How do DREs cooperate?
![Page 9: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/9.jpg)
Experimental setup
4
![Page 10: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/10.jpg)
Experimental setup
4
![Page 11: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/11.jpg)
Experimental setup
4
TCDD
Luciferase
![Page 12: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/12.jpg)
1D data shows cooperativity of binding sites
5
ABCD T
relat
ive lu
cifer
ase
activ
ity [R
LU]
1
2
3
TCDD [nM]100 101 102
AAA
AA
AAA AA
A
A AA
BBBBBBBB B B B B B B
Active Sites
![Page 13: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/13.jpg)
1D data shows cooperativity of binding sites
5
ABCD T
relat
ive lu
cifer
ase
activ
ity [R
LU]
1
2
3
TCDD [nM]100 101 102
AAA
AA
AAA AA
A
A AA
BBBBBBBB B B B B B B
Active SitesABAB
AB
ABABAB
AB
AB
ABAB
AB AB
AB
AB
![Page 14: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/14.jpg)
Modeling approach
6
promoter logic
Bintu, L. et al. Curr. Opin. Genet. Dev. 15, 116–124 (2005).
![Page 15: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/15.jpg)
Modeling approach
6
promoter logic
XYKPKXKY
Bintu, L. et al. Curr. Opin. Genet. Dev. 15, 116–124 (2005).
![Page 16: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/16.jpg)
Modeling approach
6
promoter logic
XYKPKXKY
EX
EY
Bintu, L. et al. Curr. Opin. Genet. Dev. 15, 116–124 (2005).
![Page 17: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/17.jpg)
Modeling approach
6
promoter logic
XYKPKXKY
EX
EY
EXY
Bintu, L. et al. Curr. Opin. Genet. Dev. 15, 116–124 (2005).
![Page 18: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/18.jpg)
Interpretation of resulting model parameters
7
strongest binding sites recruit RNA Polymerase
B site most important cooperation partner
ABCD
![Page 19: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/19.jpg)
Interpretation of resulting model parameters
7
strongest binding sites recruit RNA Polymerase
B site most important cooperation partner
ABCD
![Page 20: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/20.jpg)
Interpretation of resulting model parameters
7
strongest binding sites recruit RNA Polymerase
B site most important cooperation partner
ABCD
![Page 21: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/21.jpg)
Interpretation of resulting model parameters
7
strongest binding sites recruit RNA Polymerase
B site most important cooperation partner
ABCDHow are 2 signals integrated?
![Page 22: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/22.jpg)
CYP1A1 expression modulated by ß-catenin & TCDD
8Braeuning, A., Köhle, C., Buchmann, A. & Schwarz, M. Toxicol. Sci. 122, 16–25 (2011).
TCDD –
ß-catenin +
–
–
+
–
+
+
*
*175
125
75
1
0
55.1c
CYP1A1
rela
tive m
RN
A e
xpre
ssio
n [a
. u.]
![Page 23: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/23.jpg)
CYP1A1 expression modulated by ß-catenin & TCDD
8Braeuning, A., Köhle, C., Buchmann, A. & Schwarz, M. Toxicol. Sci. 122, 16–25 (2011).
AhR expression not modulated by ß-catenin & TCDD
TCDD –
ß-catenin +
–
–
+
–
+
+
*
*175
125
75
1
0
55.1c
CYP1A1
rela
tive m
RN
A e
xpre
ssio
n [a
. u.]
0
0.4
0.6
1AhR
![Page 24: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/24.jpg)
Experimental setup
9
ß-catenin
TCDD
Luciferase
![Page 25: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/25.jpg)
Experimental setup
9
ß-catenin
TCDD
Luciferase
![Page 26: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/26.jpg)
2D data shows interplay of ß-catenin & TCDD
10
ATBCD (WT)
ßòJH[LUPU
�HJ[P]P[`�B�
D 100
93
67
53
29
28
;*++�BU4D100 101 1020
ABCD
;*++�BU4D100 101 1020
AT5
4
3
2
1
SVN�YLS��S\J��HJ[P]P[`�B93<D
;*++�BU4D100 101 1020
DATA
ABCD T
![Page 27: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/27.jpg)
2D data shows interplay of ß-catenin & TCDD
10
PL model unable to describe ß-catenin integration
ATBCD (WT)
ßòJH[LUPU
�HJ[P]P[`�B�
D 100
93
67
53
29
28
;*++�BU4D100 101 1020
ABCD
;*++�BU4D100 101 1020
AT5
4
3
2
1
SVN�YLS��S\J��HJ[P]P[`�B93<D
;*++�BU4D100 101 1020
DATA
ABCD T
ßòJH[LUPU
�HJ[P]P[`�B�
D 100
93
67
53
29
28
;*++�BU4D100 101 1020
;*++�BU4D100 101 1020
;*++�BU4D100 101 1020
SVN�YLS��S\J��HJ[P]P[`�B93<D
5
4
3
2
1MO
DEL
![Page 28: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/28.jpg)
2D data shows interplay of ß-catenin & TCDD
10
PL model unable to describe ß-catenin integration
ATBCD (WT)
ßòJH[LUPU
�HJ[P]P[`�B�
D 100
93
67
53
29
28
;*++�BU4D100 101 1020
ABCD
;*++�BU4D100 101 1020
AT5
4
3
2
1
SVN�YLS��S\J��HJ[P]P[`�B93<D
;*++�BU4D100 101 1020
DATA
ABCD T
ßòJH[LUPU
�HJ[P]P[`�B�
D 100
93
67
53
29
28
;*++�BU4D100 101 1020
;*++�BU4D100 101 1020
;*++�BU4D100 101 1020
SVN�YLS��S\J��HJ[P]P[`�B93<D
5
4
3
2
1MO
DEL
![Page 29: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/29.jpg)
Modeling approach – adding TF formation
11
XYKPKXKY
EX
EY
EXY
promoter logic
Bintu, L. et al. Curr. Opin. Genet. Dev. 15, 116–124 (2005).
![Page 30: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/30.jpg)
Modeling approach – adding TF formation
11
XYKPKXKY
EX
EY
EXYAhR Arnt
TCDD ß-catenin
promoter logictranscription factor formation +
Bintu, L. et al. Curr. Opin. Genet. Dev. 15, 116–124 (2005).
![Page 31: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/31.jpg)
PL + TFF model capture dual signal integration
12
ATBCD (WT)
ßòJH[LUPU
�HJ[P]P[`�B�
D 100
93
67
53
29
28
;*++�BU4D100 101 1020
ABCD
;*++�BU4D100 101 1020
AT5
4
3
2
1
SVN�YLS��S\J��HJ[P]P[`�B93<D
;*++�BU4D100 101 1020
DATA
ßòJH[LUPU
�HJ[P]P[`�B�
D 100
93
67
53
29
28
;*++�BU4D100 101 1020
;*++�BU4D100 101 1020
;*++�BU4D100 101 1020
SVN�YLS��S\J��HJ[P]P[`�B93<D
5
4
3
2
1MO
DEL
ABCD T
![Page 32: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/32.jpg)
Conclusions
13
‣ Cooperativity of CYP1A1 promoter binding sites‣ 2 strongest binding sites control recruitment of RNAP
‣ second DRE is most important cooperation partner
‣ Dual signal integration on CYP1A1 promoter‣ simple promoter logic not sufficient to capture effect of
ß-catenin on CYP1A1 expression‣ additional transcription factor formation necessary‣ combined models capture dual signal integration
![Page 33: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/33.jpg)
Conclusions
13
‣ Cooperativity of CYP1A1 promoter binding sites‣ 2 strongest binding sites control recruitment of RNAP
‣ second DRE is most important cooperation partner
‣ Dual signal integration on CYP1A1 promoter‣ simple promoter logic not sufficient to capture effect of
ß-catenin on CYP1A1 expression‣ additional transcription factor formation necessary‣ combined models capture dual signal integration
![Page 34: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/34.jpg)
Conclusions
13
‣ Cooperativity of CYP1A1 promoter binding sites‣ 2 strongest binding sites control recruitment of RNAP
‣ second DRE is most important cooperation partner
‣ Dual signal integration on CYP1A1 promoter‣ simple promoter logic not sufficient to capture effect of
ß-catenin on CYP1A1 expression‣ additional transcription factor formation necessary‣ combined models capture dual signal integration
![Page 35: Binding site cooperativity and dual signal integration in CAP1A1 induction](https://reader031.vdocument.in/reader031/viewer/2022021506/587ce8541a28ab564b8b4a0b/html5/thumbnails/35.jpg)
Acknowledgements
‣ Nils Blüthgen‣ Pawel Durek‣ Raphaela
Fritsche‣ Manuela
Benary‣ Anja Sieber
‣ Nadine Schmidt‣ Kajetan Bentele‣ Bertram Klinger‣ Johannes Meisig‣ Jörn Schmiedel‣ Franziska Witzel
Systems Biology of Molecular Networks Group @ Charité
‣ Michael Schwarz‣ Albert Braeuning‣ Alexandra Löffler
Department of Toxicology @ Uni Tübingen
Funding
14