Transcription Factors … (TF) Transcription in eukaryote -controlled by trans-acting protein … TF -more complex than in prokaryotes

Transcription Factors … (TF) TF Binding at cis-acting regulatory sequences Can be repressosr ar activators Located much farther from promoter kb up/down stream Alternative controlled

Alternative controlled Transthyretin (TTR)..steroid hormone transporter 2 control elements okb upstream element 200 bp upstream Turn the gene on in two different cell types hepatocytes choroid plexus cells

How to get the gene of TF 1.Detection of the controlled elements … 5 ’ deletion assay 2.Biochemical isolation of TF -several chromatographic steps with cell extract …....get cognate proteins -Dnase footprint or mobility shift assay …....get specific DNA binding proteins -sequence-specific DNA affinity chromatography …...get a purified protein 3.In vivo transcription activation … to confirm protein function 4.Partial amino acid sequence determination and gene cloning 5.In vivo assay of the TF gene activity

Detection of the controlled elements 5 ’ -deletion analysis

fractions collected DNase footprint/mobility shift assay Several chromatographic steps with cell extract … get cognate proteins Retardation assay Dnase footprint

DNase footprint assay Biochemical isolation of TF Interesting fractions = 9-12

Mobility shift assay Gel retardation assay Biochemical isolation of TF

fractions 9-12 purified protein Sequence-specific DNA affinity chromatography …...get a purified protein Specific regulatory sequence In vivo transcription activation assay

In vitro transcription activation … to confirm protein function SP1 binding site in SV40 genome No SP1 binding site on adenovirus SP1 RNA SP1 protein has no effect on transcription from the adenovirus promoterbut stimulate transcription from SV40 promoter about 10 folds.

isolated TF partial protein sequences oligonucleotide probe TF gene

To test the gene function ….in vivo assay

General structure of TF Study by in vitro translation and N-terminal deletion assay 2 functional domains found UAS = upstream activating sequence

General Structure of TF 2 functional domains DNA – binding domain … interact with specific DNA sequence Activation domain … interact with other proteins

5 structural types of DNA binding domain 1.Homeodo main (helix- turn- helix) 2.Zinc- finger protein 3.Winged- helix (fork- head) 4.Leucine zipper 5.Helix- loop-helix

Homeodomain ( helix-turn- helix ) The name derived from a group of Drosophila genes in which the conserved sequence encoding this structural domain was first noted. Homeotic genes, mutation in these genes resulted in the transformation of one body part into another during the development. Two of most-studied of these genes Antennapedia (Antp) Ultrabithorax (Ubx) normal fly mutant fly

Structure of homeodomain

Helix-Turn-Helix protein and Homeoboxes -Three  -helical regions separated by short turns. -Bind to DNA in similar manner. -Bind as dimers -Amino acid substitution in the  helices near C terminal disturb the binding in major groove of DNA -The region encoding about 60 amino acids was remarkably conserved in all these genes called homeobox. Homeobox = region in the gene Homeotic gene = gene Homeodomain / helix-turn-helix protein = protrein encoded by homeotic gene

Example of helix-turn-helix proteins Gene productOrganismFunctions MAT  1yeastactivates  -specific genes MAT  2yeastinactivates a-specific genes MAT a1yeast combined with  2 repressed haploid-specific genes AntennapediaDrosophilahomeotic gene UltrabithoraxDrosophila homeotic gene Engrailed Drosophilasegment-polarity gene PairedDrosophilapair-rule gene Fushi tarazuDrosophilapair-rule gene HOXmousedevelopmental regulators Unc86C. elegansdetermine cell lineage in worms Oct1humangenerally distributed activator Oct2humanlymphoid-specific activator Pitmousepituitary-specific activator

Determine the fate of each segments (mouth, legs, wings,etc.)

The 9 homeotic genes in fly Bithorax complex (Bx-C) Ultrabithorax (Ubx) Abdominal A (abdA) Abdominal B (abdB) Antennapedia complex (Ant-C) labial (lab) Prodoscipedia (pb) Deformed (Dfd) Sex combs reduced (Scr) Antennapedia (Antp) Engrailed

Example of homeotic genes in mouse and human Pit-1 mutant Growth hormone deficiency

Example of homeotic genes in plant 3 classes of floral organ- identity genes in Arabidopsis, A B and C, encoded TF of MADS family