Gene expression is the process where information in DNA is used to create a functional product, like a protein, through transcription. In eukaryotic cells, an enzyme called RNA polymerase II copies a segment of DNA into RNA. For this to begin, general transcription factors must assemble on the DNA, including Transcription Factor II A (TFIIA). TFIIA is a protein complex that helps initiate transcription for all protein-coding genes.
Structural Composition of TFIIA
TFIIA is a multi-subunit protein complex whose structure varies slightly across organisms. In humans, TFIIA is assembled from the products of two genes. The GTF2A1 gene produces the large subunit, while the GTF2A2 gene produces the small γ (gamma) subunit. The protein product of GTF2A1 is a precursor that undergoes proteolytic processing, where it is cleaved into two pieces.
This cleavage results in the α (alpha) and β (beta) subunits. These two subunits remain associated, forming the large α/β subunit. The complete human TFIIA complex is a heterotrimer, composed of the α/β subunit and the γ subunit. The subunits interact to form a structure with distinct domains that are integral to its function.
Core Function in Transcription Initiation
The main role of TFIIA is to facilitate the assembly of the preinitiation complex (PIC) at the start of a gene. This process begins at a DNA sequence called the TATA box, located in the promoter region. The PIC’s assembly is initiated when the TATA-binding protein (TBP), a component of the larger TFIID complex, binds to the TATA box.
TFIIA enters the process by binding to the TBP subunit of TFIID after TBP has bound to the DNA. The binding of TFIIA to the TBP-DNA complex acts like a clamp, preventing TBP from detaching from the TATA box and strengthening the PIC’s foundation. This stabilization helps in the subsequent recruitment of other general transcription factors to the promoter.
The binding of TFIIA to the TBP-DNA complex induces a conformational change in TBP. This creates a proper binding surface for the next general transcription factor, TFIIB. The arrival of TFIIB further solidifies the PIC and helps position RNA polymerase II correctly at the gene’s start site.
While TFIIA does not bind to DNA directly, it can make contact with DNA sequences near the TATA box in some contexts. A specific DNA sequence known as a TFIIA recognition element (IIARE) has been identified in many human promoters. The presence of a IIARE can enhance the binding of TFIIA, suggesting a more direct role in promoter binding than previously understood.
Regulatory Role in Gene Activation
Beyond its structural role in PIC assembly, TFIIA actively regulates gene expression. It can function as an anti-repressor by counteracting negative regulatory factors that inhibit transcription. One such regulator is Negative Cofactor 2 (NC2), a protein complex that also binds to TBP. When NC2 is bound to TBP at a promoter, it stalls PIC assembly and represses transcription.
TFIIA can actively displace NC2 from the TBP-DNA complex. This competition between TFIIA and NC2 for binding to TBP represents a regulatory switch. By displacing the repressor, TFIIA allows PIC assembly to proceed, which turns on or increases the gene’s expression. This function shows TFIIA is an active participant in transcription.
TFIIA also functions as a coactivator, bridging the general transcription machinery and gene-specific activator proteins. These activators bind to DNA sequences called enhancers to increase transcription and can recruit TFIIA to the promoter. This enhances TFIIA’s ability to stabilize the TBP-DNA complex, providing a mechanism for fine-tuning gene expression in response to cellular signals.
The interaction with activators highlights the dynamic nature of TFIIA’s involvement in transcription. Its presence at a promoter is not constant and can be influenced by other regulatory proteins. By mediating signals from activators, TFIIA helps ensure that genes are transcribed at appropriate levels and times, a function beyond its mechanical role.