We’ve briefly covered the initiation of transcription but the process is more complex than transcription factors floating to a promoter and starting up RNAPII. In thermodynamic terms (ouch, I know), the transcriptional activator proteins shift the equilibrium of free transcription factors to the formation of the preinitiation complex (PIC): these activators increase or decrease the association rate of proteins and affect the formation of the PIC. Proteins can affect transcription initiation by altering accessibility to the promoter or changing the stability of the PIC. Activators (also called transcription factors and gene regulatory proteins) bind to specific DNA sequences and promote transcription. Co-activators interact with these activators to promote transcription, without interacting directly with the DNA. Essentially, activators and co-activators function to recruit, position, and modify GTFs and RNAPII by altering the transcriptional machinery, bending the DNA, or changing the chromatin structure.
Regulatory elements are important in eukaryotes and come in several forms. The core promoter contains the start site of transcription and the TATA box. Here is where GTFs and RNAPII bind to form the PIC. The proximal promoter (or the upstream activator sequence in yeast) is located within 200 bp upstream of the start site and contains sites for regulatory factors to bind. Finally, enhancer sequences exist from 200 to 50 000 bp from the start site and can also bind regulatory factors. Enhances act independent of function, and they can act at a distance due to DNA looping.
What are the components of a transcriptional activator protein?
TAD: trans-activation domain
DBD: DNA-binding domain
NLS: nuclear localization signal
Regulatory domains: catalytic function of the activator protein
Dimerization domain: for dimerization of activators (especially important for DNA-binding)
The DNA-binding domain can read DNA sequences and has several structural motifs: the helix-turn-helix (HTH), homeodomain, zinc finger, basic leucine zipper, and helix-loop-helix. In general, these domains contain an alpha helix that fits snuggly in the major groove of the DNA and makes specific contacts with the DNA. These DBDs can thereby recognize response elements in the DNA to carry out their functions.
The helix-turn-helix motif binds DNA as a monomer and recognizes DNA via a C-terminal helix, and the N-terminal helix positions the C-terminal helix in the major groove of the DNA. In contrast, the homeodomain binds DNA as a monomer and contains three helices, one of which binds the DNA and the other two bind other proteins or the DNA backbone.
The zinc finger motif uses a zinc ion to coordinate the structure of the protein. The Cys2/His2 zinc finger motifs act as a monomer or a dimer and use cysteine and histidine to coordinate the zinc and bind the DNA major groove. Additionally, Cys4 zinc finger motifs also act as monomers or dimers and coordinate the zinc with four cysteine residues to allow for DNA interactions. The basic helix-loop-helix domain and leucine zipper motifs are additional DNA-binding motifs that act as dimers and are commonly found in DNA-binding proteins.