Transcription Factors Charles Carey!
Fred Hutchinson Cancer Research Center!
[email protected] Gompel and Prud’homme Developmental Biology. 6th edi9on. Sco< Gilbert. chapter 9. 1 - Transcription factors and cis
regulatory sequences!
2 – Transcription factors and
enhancer modules - examples!
3 - Gene regulatory networks!
Today Classes of transcription factors!
Transcription factors bind DNA Chen, F. E. et al., Crystal Structure of p50/p65 Heterodimer of Transcrip<on Factor NF-­‐kappa B bound to DNA, Nature, 391, pp.410 (1998) pics : h<p://www.biochem.umd.edu/biochem/kahn/molmachines/enhancesomes/NFkB.html Transcription in context Today DNA – basal transcription factors!
Eukaryotic gene anatomy!
Cis regulatory elements!
Clusters of cis regulatory elements =!
Enhancers / switches / cis regulatory modules!
( Cis? Trans? )!
Txn factors Enhancer Sequence General transcrip9on factors Basal promoter Transcribed region Txn factors / enhancer interact with general txn
factors at basal promoter, recruit RNA Pol II complex!
Transcription factors and ʻenhancersʼ
can also repress or silence transcription !
Co-­‐repressors Kornberg, RD. 1999. Eukaryo9c transcrip9onal control. Trends in Cell Biology 9(12):M46-­‐M49 Nowak SJ, Corces VG. Trends Genet. 2004 Apr;20(4):214-­‐20. Insulators, LCRs : domains of gene activity Today Transcription factors bind DNA at!
Enhancers!
Define cis, trans!
Summary (1) 1. DNA binding proteins!
2. Early embryogenesis – made from
maternal mRNA!
3. Sequence specific DNA binding but
require cooperativity!
4. Often work at distance (looping)!
5. Activate OR Repress transcription!
Other regulators of transcription?!
2 - examples of gene
regulation by txn factors patterning D A P V Hong JW., Hendrix DA., Papatsenko D., Levine MS. 2008. Dec23; 105
(51):20072-­‐6. dorsal !
Drosophila melanogaster version
of NF-kappaB p65 subunit txn factors work together
combinatorially at cis modules (zen = Hox3) Levine Lab (Hong et. al.) dorsal transcription factor
works in a gradient D A P V Roth, S. Stein, D., Nusslein-­‐Vollhard, C. 1989. Cell vol. 59, 1189-­‐1202. Levine Lab (Hong et. al.) ID of regulatory elements ( from B::lacZ ) B lacZ coding region Minimal promoter Enhancer modularity at yellow gene:!
Gain (and loss) of function in wing!
Loss of function in abdomen Prud’homme et. al. 2006. Nature 440, 1050-­‐1053 Carroll et. al. Regula9ng Evolu9on. Sci. American. May 2008: 61-­‐67. Enhancer modularity at Duffy gene :!
Malaria, W. Africa Carroll et. al. Regula9ng Evolu9on. Sci. American. May 2008: 61-­‐67. Summary (2)!
Examples of gene regulation 1.  Combinatorial action at enhancers.!
2.  Modularity of enhancers.!
3.  Easier to tinker with development
by tinkering with enhancers? Vs.
proteins?!
3 – gene regulatory
networks!
When several transcription factors, !
genes in process - gets complicated !
dorsal gradient as !
gene regulatory network Need pic Stathopoulos A, Levine M. 2002. Dorsal Gradient Networks in Drosophila embryo. Developmental Biology 246, 57–67 (2002) dorsal gene regulatory network dorsal
ectoderm /
neurogenic!
ectoderm!
dorsal ventral
neurogenic!
ectoderm mesoderm gastrulation Levine, M., Davidson, E. 2005. Gene Regulatory Networks for Development. Proc Natl Acad Sci U S A. 2005 April 5; 102(14): 4936–4942. Summary (3) 1.  Gene regulatory networks : a way to
make sense of regulatory gene in/
output.!
2.  May facilitate comparisons between
developmental programs within /
between taxa.!
3.  Few examples (lots of experimental
work).!