promoter: in 5' flanking seq; defines initiation site (+1); TATA box (-25); CAT box (-75); deviations from the consensus sequence lead to strong or weak signals
enhancers: seen in 5' flanking, 3' flanking, or in gene itself; interacts with trans-acting factors with distinct enhancers recruiting distinct protein factors allowing for regulated transcription
Protein Factors (trans-acting factors)
proteins affecting transcription
recognize specific DNA target sequence
a protein with at least 2 functional domains: active domain and DNA binding domain (recognizes specific DNA seq); active domain can interact directly or indirectly
Zinc Finger Proteins
TFIIIA with 9 Zn fingers
Þ transcription factor for RNA poly III (tRNA)
Each finger has 2 cys and 2 His which coordinate a Zn atom
Binds to DNA and activates it
Þ binds within gene itself
The fingers insert into the major grooves of DNA
Steroid Hormone Receptors
These transcriptional factors interact with hormones in the cytoplasm and then the receptor/hormone complexes migrate to the nucleus where they are able to interact with distinct DNA sequence
Has DNA binding domain, activation domain and hormone binding domain
DNA binding domain cannot interact with DNA sequence unless hormone is bound
Exist as palindromes
Leucine Zipper Proteins
Recognize DNA as dimers and bind to palindrome sequences
Dimerization domain, with stretches of leucine residues forming a zipper which interacts hydrophobically
Has DNA binding domain, activation domain and a dimerization domain (Leu zipper)
Binds to major groove
JAK – STAT pathway
JAK = kinase; STAT = transcription factor
The ligand itself does not enter the cell!!
Þ the signal created upon ligand binding to the receptor is propogated to defined effect in the nucleus!
STATs are activated by phosphorylation by kinase: forms a stat dimer and causes them to enter nucleus and activate transcription
Homeobox Genes
Particular region of a protein or protein domain
Critical to correct development
Region within embryo has a particular homeobox gene expressed becomes different structures in adult
Amazing conservation of function of these genes
Þ seen in drosophila, mouse, frog, even yeast!
Interacts with both major and minor groove
Summary
These transcriptional factors do not work alone, but act in concert with one another
Þ synergy
One regulatory step
Post Transcriptional Regulation
Alternative Splicing
mRNA Stability
mRNA meet steady states
Balance btwn transcription rates, processing events, and mRNA degradation gives rise to the steady state