1 / 31

Understanding and Predicting Transcription Factor Specificities

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

corina
Download Presentation

Understanding and Predicting Transcription Factor Specificities

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Understanding and Predicting Transcription Factor Specificities Richard S. Mann C2B2/MAGNet Center Third Annual Retreat April 11, 2008

  2. Signal Transduction

  3. Transcriptional control by multiprotein complexes p65 p50 • Signal integration • Vast combinatorial ensembles with a • min number of factors • Evolvability from Wolberger C., 1999

  4. Drosophila Hox genes Abd-B lab abd-A Dfd Ubx Scr Antp Dave Kosman, UCSD

  5. D. melanogaster zen bcd ftz lab pb Dfd Scr Antp Ubx abd-A abd-B A P Hoxa1 Hoxa2 Hoxa3 Hoxa4 Hoxa5 Hoxa6 Hoxa7 Hoxa9 Hoxa10 Hoxa11 Hoxa13 Mus musculus Hoxb1 Hoxb2 Hoxb3 Hoxb4 Hoxb5 Hoxb6 Hoxb7 Hoxb8 Hoxb9 Hoxa13 Hoxc4 Hoxc5 Hoxc6 Hoxc8 Hoxc9 Hoxc10 Hoxc11 Hoxc12 Hoxc13 Hoxd1 Hoxd3 Hoxd4 Hoxd8 Hoxd9 Hoxd10 Hoxd11 Hoxd12 Hoxd13 Hox factors: molecular architects of morphological diversity thorax abdomen head Adapted from Perason J.C. et al., 2005

  6. Problem of Hox specificity: Paradox 1 Homeodomain linker N-term arm helix 1 helix 2 helix 3 YPWM 1 10 20 30 40 50 60 Lab TYKWMQ(109)NNSGRTNFTNKQLTELEKEFHFNRYLTRARRIEIANTLQLNETQVKIWFQNRRMKQKKRV Pb EYPWMK(28) PRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQVKVWFQNRRMKHKRQT Dfd IYPWMK(17) PKRQRTAYTRHQILELEKEFHYNRYLTRRRRIEIAHTLVLSERQIKIWFQNRRMKWKKDN Scr IYPWMK(14) TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH Antp LYPWMR (8) RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN Ubx FYPWMA (7) RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI Abd-A RYPWMT(24) RRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKEL Abd-B LHEWTG (3) VRKKRKPYSKFQTLELEKEFLFNAYVSKQKRWELARNLQLTERQVKIWFQNRRMKNKKNS identical residues make DNA contacts Paradox 2: most Hox proteins bind to very similar ‘AT’ rich binding sites

  7. Paradox 3: residues important for specificity are usually disordered Ubx YPWM Exd Passner, Aggarwal

  8. } D. Andrew; BioEssays 23:901-911 A P Fkh Salivary Gland

  9. Distinct properties of Hox-Exd binding sites fkh250 fkh250con Exd Hox Exd Scr AGATTTATGG AGATTAATCG paralog specific shared Ryoo et al., 1999

  10. fkh250 fkh250con His–12 Arg3 Passner, Jain, Aggarwal

  11. fkh250 has two minor groove width minima that dictate electrostatic potential Rohs, Sosinsky, Honig

  12. Recognition of DNA SHAPE ‘Specific’ Hox-DNA contacts Base-specific hydrogen bonds ‘General’ Hox-DNA contacts homeodomain linker N-term arm helix 1 helix 2 helix 3 YPWM

  13. ‘Specific’ Hox-DNA contacts ‘General’ Hox-DNA contacts homeodomain linker N-term arm helix 1 helix 2 helix 3 YPWM

  14. ‘Specific’ Hox-DNA contacts ‘General’ Hox-DNA contacts homeodomain linker N-term arm helix 1 helix 2 helix 3 YPWM What are the global DNA binding specificities? What are the range of DNA recognition modes? How general is this mechanism?

  15. ‘Specific’ Hox-DNA contacts ‘General’ Hox-DNA contacts homeodomain linker N-term arm helix 1 helix 2 helix 3 YPWM What are the global DNA binding specificities? What are the range of DNA recognition modes? How general is this mechanism?

  16. LINKER YPWM HOMEODOMAIN His–12 and Arg3 are among Scr’s ‘signature’ residues His–12 Arg3

  17. Paralog-specific ‘signature’ residues surrounding the YPWM motif Lab SSIPTYKWMQLKRNVP XD1 SYVSTFDWMKVKRNPP mA1 SPAQTFDWMKVKRNPP hB1 PTARTFDWMKVKRNPP xA1 GPTQTFDWMKVKRNPP CB1 SRARTFDWMKVKRNPP MB1 LTPRTFDWMKVKRNPP PB DSVPEYPWMKEKKTSR HB2 PPAPEFPWMKEKKSAK HB3 LTKQIFPWMKESRQTS HD3 ISKQIFPWMKESRQNS MB3 LTKQIFPWMKESRQTS DFD GERIIYPWMKKIHVAG CD4 QPAVVYPWMKKVHVNS MD4 QPAVVYPWMKKVHVNS HD4 QPAVVYPWMKKVHVNS MA4 KEPVVYPWMKKIHVSA HA4 KEPVVYPWMKKIHVSA CA4 KEPVVYPWMKKIHVST CB4 KEPVVYPWMKKVHVST MB4 KEPVVYPWMRKVHVST HC4 KQPIVYPWMKKIHVST MC4 KQPIVYPWMKKIHVST XB4 QDPVVYPWMKKAHISK Scr NPPQIYPWMKRVHLGT MA5 AQPQIYPWMRKLHISH HA5 AQPQIYPWMRKLHISH MB5 QTPQIFPWMRKLHISH HB5 QSPQIFPWMRKLHINH XB5 QSPQIFPWMRKLHINH HC5 QPPQIYPWMTKLHMSH ANT MPSPLYPWMRSQPGKC CB8 SPTQLFPWMRPQAAAG MB8 SPTQLFPWMRPQAAAG XB8 SPTQLFPWMRPQAAGR CD8 SPAQMFPWMRPQAAPG MD8 SPSQMFPWMRPQAAPG MC8 SPSLMFPWMRPHAPGR UBX SNHTFYPWMAIAGECP XB7 ANLRIYPWMRSAGADR HB7 SNFRIYPWMRSSGTDR MB7 SNFRIYPWMRSSGPDR XA7 SHFRIYPWMRSSGPDR CA7 ANFRIYPWMRSSGPDR MA7 ASFRIYPWMRSSGPDR ABA ADLPRYPWMTLTDWMG MC6 ASIQIYPWMQRMNSHS HC6 ASIQIYPWMQRMNSHS XC6 GSIQIYPWMQRMNSHS MB6 CSTPVYPWMQRMNSCN HB6 CSTPVYPWMQRMNSCN Lab Pb Dfd Scr Antp Ubx AbdA Hox6

  18. Fkh250 Scr Kd ~10nM Kd ~12nM Dfd Kd ~20nM Kd ~40nM Ubx Kd >300nM Kd ~30nM Fkh250con

  19. Fkh250 Dfd is a repressor of fkh250 Fkh250 Dfd

  20. Two steps in Hox specificity Hox Hox binding site DNA binding cofactors Hox binding site Regulation Act Rep

  21. ‘Specific’ Hox-DNA contacts ‘General’ Hox-DNA contacts homeodomain linker N-term arm helix 1 helix 2 helix 3 YPWM What are the global DNA binding specificities? What are the range of DNA recognition modes? How general is this mechanism?

  22. Cognate Sequence Identifier (CSI) Aseem Ansari

  23. Correlation between Exd and Dfd binding Karl Haucshild and Aseem Ansari

  24. Exd+Scr Exd+Ubx Sequences that prefer Scr-Exd Sequences that prefer Ubx-Exd

  25. Exd Dfd Karl Haucshild and Aseem Ansari

  26. ‘Specific’ Hox-DNA contacts ‘General’ Hox-DNA contacts homeodomain linker N-term arm helix 1 helix 2 helix 3 YPWM What are the global DNA binding specificities? What are the range of DNA recognition modes? How general is this mechanism?

  27. Dfd Exd fkh250 Lab Exd Lab48/95 ? Ubx Exd DllR AbdA Exd DllR AbdA En DllR Hox cofactor DNA Scr Exd fkh250 Xiangshu Jin

  28. Lab Ebner Lab DNA shape varies among Hox binding sites Fkh250con Fkh250 All Hox? Scr, Dfd DllR Lab48/95 Ubx, AbdA Lab Remo Rohs, Barry Honig

  29. ‘Specific’ Hox-DNA contacts ‘General’ Hox-DNA contacts homeodomain linker N-term arm helix 1 helix 2 helix 3 YPWM What are the global DNA binding specificities? What are the range of DNA recognition modes? How general is this mechanism?

  30. Rohit Joshi Jonathan Passner Rinku Jain Aneel Aggarwal Remo Rohs Alona Sosinsky Barry Honig Xiangshu Jin Karl Hauschild Aseem Ansari Andrea Califano

More Related