understanding and predicting transcription factor specificities
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Understanding and Predicting Transcription Factor Specificities. Richard S. Mann C2B2/MAGNet Center Third Annual Retreat April 11, 2008. Signal Transduction. Transcriptional control by multiprotein complexes. p65. p50. Signal integration Vast combinatorial ensembles with a - PowerPoint PPT PresentationTRANSCRIPT
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Understanding and Predicting Transcription Factor Specificities
Richard S. MannC2B2/MAGNet Center Third Annual Retreat
April 11, 2008
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Signal Transduction
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Transcriptional control by multiprotein complexes
p50 p65
Signal integration
Vast combinatorial ensembles with a min number of factors
Evolvability
from Wolberger C., 1999
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Dave Kosman, UCSD
Drosophila Hox genes
lab
DfdScr Antp
Ubx
abd-A
Abd-B
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Hox factors: molecular architects of morphological diversity
lab pb Dfd
zen bcd
Scr Antp
ftz
Ubx abd-A abd-B
D. melanogaster
Hoxd1 Hoxd4 Hoxd8 Hoxd9 Hoxd10 Hoxd11 Hoxd12 Hoxd13Hoxd3
Hoxa1 Hoxa2 Hoxa4 Hoxa5 Hoxa6 Hoxa7 Hoxa9 Hoxa10 Hoxa11 Hoxa13Hoxa3
Hoxb1 Hoxb2 Hoxb4 Hoxb5 Hoxb6 Hoxb7 Hoxb8 Hoxb9 Hoxa13Hoxb3
Hoxc4 Hoxc5 Hoxc6 Hoxc8 Hoxc9 Hoxc10 Hoxc11 Hoxc12 Hoxc13
Mus musculus
A P
Adapted from Perason J.C. et al., 2005
head thorax abdomen
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Problem of Hox specificity: Paradox 1
identical residues make DNA contacts
YPWM helix 1 helix 2 helix 3
Homeodomain
linker N-term arm
1 10 20 30 40 50 60Lab TYKWMQ(109)NNSGRTNFTNKQLTELEKEFHFNRYLTRARRIEIANTLQLNETQVKIWFQNRRMKQKKRVPb EYPWMK(28) PRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQVKVWFQNRRMKHKRQTDfd IYPWMK(17) PKRQRTAYTRHQILELEKEFHYNRYLTRRRRIEIAHTLVLSERQIKIWFQNRRMKWKKDNScr IYPWMK(14) TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHAntp LYPWMR (8) RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENUbx FYPWMA (7) RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIAbd-A RYPWMT(24) RRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELAbd-B LHEWTG (3) VRKKRKPYSKFQTLELEKEFLFNAYVSKQKRWELARNLQLTERQVKIWFQNRRMKNKKNS
Paradox 2: most Hox proteins bind to very similar ‘AT’ rich binding sites
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Passner, Aggarwal
Ubx
Exd
YPWM
Paradox 3: residues important for specificity are usually disordered
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}Salivary Gland
D. Andrew; BioEssays 23:901-911
A
P
Fkh
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Distinct properties of Hox-Exd binding sites
fkh250 fkh250con
Ryoo et al., 1999
Exd Scr
AGATTAATCG
paralogspecific
Exd Hox
AGATTTATGG
shared
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fkh250
Passner, Jain, Aggarwal
fkh250con
His–12
Arg3
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fkh250 has two minor groove width minima that dictate electrostatic potential
Rohs, Sosinsky, Honig
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YPWM helix 1 helix 2 helix 3
homeodomainlinker N-term
arm
‘General’ Hox-DNA contacts
Base-specific hydrogen bonds
‘Specific’ Hox-DNA contacts
Recognition of DNA SHAPE
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YPWM helix 1 helix 2 helix 3
homeodomainlinker N-term
arm
‘General’ Hox-DNA contacts‘Specific’ Hox-DNA contacts
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YPWM helix 1 helix 2 helix 3
homeodomainlinker N-term
arm
‘General’ Hox-DNA contacts‘Specific’ Hox-DNA contacts
What are theglobal DNA
binding specificities?How general is
this mechanism?
What are therange of DNA
recognition modes?
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YPWM helix 1 helix 2 helix 3
homeodomainlinker N-term
arm
‘General’ Hox-DNA contacts‘Specific’ Hox-DNA contacts
What are theglobal DNA
binding specificities?How general is
this mechanism?
What are therange of DNA
recognition modes?
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His–12 and Arg3 are among Scr’s ‘signature’ residues
HOMEODOMAINLINKERYPWM
His–12 Arg3
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Lab SSIPTYKWMQLKRNVPXD1 SYVSTFDWMKVKRNPPmA1 SPAQTFDWMKVKRNPPhB1 PTARTFDWMKVKRNPPxA1 GPTQTFDWMKVKRNPPCB1 SRARTFDWMKVKRNPPMB1 LTPRTFDWMKVKRNPPPB DSVPEYPWMKEKKTSRHB2 PPAPEFPWMKEKKSAKHB3 LTKQIFPWMKESRQTSHD3 ISKQIFPWMKESRQNSMB3 LTKQIFPWMKESRQTSDFD GERIIYPWMKKIHVAGCD4 QPAVVYPWMKKVHVNSMD4 QPAVVYPWMKKVHVNSHD4 QPAVVYPWMKKVHVNSMA4 KEPVVYPWMKKIHVSAHA4 KEPVVYPWMKKIHVSACA4 KEPVVYPWMKKIHVSTCB4 KEPVVYPWMKKVHVSTMB4 KEPVVYPWMRKVHVSTHC4 KQPIVYPWMKKIHVSTMC4 KQPIVYPWMKKIHVSTXB4 QDPVVYPWMKKAHISKScr NPPQIYPWMKRVHLGTMA5 AQPQIYPWMRKLHISHHA5 AQPQIYPWMRKLHISHMB5 QTPQIFPWMRKLHISHHB5 QSPQIFPWMRKLHINHXB5 QSPQIFPWMRKLHINHHC5 QPPQIYPWMTKLHMSHANT MPSPLYPWMRSQPGKCCB8 SPTQLFPWMRPQAAAGMB8 SPTQLFPWMRPQAAAGXB8 SPTQLFPWMRPQAAGRCD8 SPAQMFPWMRPQAAPGMD8 SPSQMFPWMRPQAAPGMC8 SPSLMFPWMRPHAPGRUBX SNHTFYPWMAIAGECPXB7 ANLRIYPWMRSAGADRHB7 SNFRIYPWMRSSGTDRMB7 SNFRIYPWMRSSGPDRXA7 SHFRIYPWMRSSGPDRCA7 ANFRIYPWMRSSGPDRMA7 ASFRIYPWMRSSGPDRABA ADLPRYPWMTLTDWMGMC6 ASIQIYPWMQRMNSHSHC6 ASIQIYPWMQRMNSHSXC6 GSIQIYPWMQRMNSHSMB6 CSTPVYPWMQRMNSCNHB6 CSTPVYPWMQRMNSCN
Lab
Pb
Dfd
Scr
Antp
UbxAbdA
Hox6
Paralog-specific‘signature’ residues
surrounding the YPWM motif
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Fkh250conFkh250
Ubx
Kd >300nM Kd ~30nM
Dfd
Kd ~40nMKd ~20nM
ScrKd ~10nM Kd ~12nM
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Fkh250DfdFkh250
Dfd is a repressor of fkh250
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Hox
Act
Rep
Hox binding site
Hox binding sitecofactors
DNA binding
Regulation
Two steps in Hox specificity
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YPWM helix 1 helix 2 helix 3
homeodomainlinker N-term
arm
‘General’ Hox-DNA contacts‘Specific’ Hox-DNA contacts
What are theglobal DNA
binding specificities?How general is
this mechanism?
What are therange of DNA
recognition modes?
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Cognate Sequence Identifier (CSI)
Aseem Ansari
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Correlation between Exd and Dfd binding
Karl Haucshild and Aseem Ansari
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Exd+Scr Exd+Ubx
Sequences that preferUbx-Exd
Sequences that preferScr-Exd
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Exd Dfd
Karl Haucshild and Aseem Ansari
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YPWM helix 1 helix 2 helix 3
homeodomainlinker N-term
arm
‘General’ Hox-DNA contacts‘Specific’ Hox-DNA contacts
What are theglobal DNA
binding specificities?How general is
this mechanism?
What are therange of DNA
recognition modes?
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Scr
Hox cofactor DNA
Exd fkh250
Lab Exd Lab48/95
Ubx Exd DllR
AbdA Exd DllR
AbdA En DllR
Dfd Exd fkh250
?
Xiangshu Jin
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Remo Rohs, Barry Honig
Fkh250con
All Hox?
Fkh250
Scr, Dfd
DllR
Ubx, AbdA
Lab48/95
Lab
DNA shape varies among Hox binding sites
Ebner
Lab
Lab
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YPWM helix 1 helix 2 helix 3
homeodomainlinker N-term
arm
‘General’ Hox-DNA contacts‘Specific’ Hox-DNA contacts
What are theglobal DNA
binding specificities?
How general is this mechanism?
What are therange of DNA
recognition modes?
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Rohit Joshi
Jonathan PassnerRinku JainAneel Aggarwal
Remo RohsAlona SosinskyBarry Honig
Xiangshu Jin
Karl HauschildAseem Ansari
Andrea Califano