In this article, I briefly describe the types of general transcription factors and their functions.
Transcription
The process of synthesis of RNA from a DNA template is called transcription. It is the first step of gene expression, in which a particular segment of DNA is copied into RNA by the enzyme RNA polymerase. In both prokaryotes and eukaryotes, the DNA→RNA transcription is the primary level at which gene expression is regulated. The stretch of DNA transcribed into an RNA molecule is called a transcription unit and encodes at least one gene. RNA polymerase is the principal enzyme responsible for RNA synthesis. It catalyzes the polymerization of ribonucleoside 5′-triphosphates as directed by a DNA template. Transcription in eukaryotic cells is more complex than that of prokaryotic cells. However, both possess the same fundamental mechanism. The transcription process begins with binding the transcription factors with the enzyme RNA polymerase.
Transcription factors
The specific proteins required for RNA polymerase II to initiate transcription are called transcription factors. Transcription factors are found in all living organisms and the number of transcription factors within an organism increases with genome size. Thus, larger genomes tend to have more transcription factors per gene. Transcription factors contain one or more DNA-binding domains (DBDs), which attach to specific sequences of DNA adjacent to the genes they regulate. It is estimated that about 5% of the genes in the human genome encode transcription factors, specifying the importance of these proteins.
Transcription factors regulate gene expression alone or with other proteins in a complex. They promote the expression of genes as activators or block the recruitment of RNA polymerase to specific genes by acting as repressors. Regulation of transcription initiation is mediated by the interplay between two classes of promoter elements. The first class includes the basal promoter elements, which can be defined as those promoter elements sufficient to direct basal levels of transcription in vitro. The second class includes the regulatory elements, which modulate the levels of transcription. The basal elements are recognized by basal transcription factors, whereas the regulatory elements are recognized by either transcriptional activators or repressors.
Eukaryotic activators are often modular, consisting of a DNA binding domain and activation domains. DNA binding domain targets the activator to the correct promoter and activation domains enhance transcription. Two types of transcription factors have been defined i.e., general transcription factors and gene-specific transcription factors. General transcription factors are involved in transcription from all polymerase II promoters and therefore constitute part of the basic transcription machinery.
General transcription factors
In eukaryotes, RNA polymerase II requires general transcription factors (GTFs) for initiation of transcription. Many of these general transcription factors are part of the large transcription pre-initiation complex and interact directly with RNA polymerase rather than binding DNA (Figure 1). The most common GTFs are TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH (figure 1).
Transcription factors are modular in structure and contain three domains, i.e., DNA binding domain, trans-activating domain, and an optional signal sensing domain. DNA binding domain attaches to specific DNA sequences (enhancer or promoter). Response elements are the DNA sequences that bind to transcription factors. Trans-activating domain (TAD), which contains binding sites for other proteins, is frequently referred to as activation functions (Afs). An optional signal sensing domain (SSD) (e.g., a ligand binding domain), senses external signals and, in response, transmits these signals to the rest of the transcription complex, resulting in up-or down-regulation of gene expression.
TFIID
The enzyme polymerase II transcribes promoters of many genes containing a sequence TATAA. The sequence is known as the TATA box, which is present 25 to 30 nucleotides upstream of the transcription start site. The general transcription factor TFIID binds to the TATA box, thus beginning the first step in the formation of a transcription complex. TFIID is a multiprotein complex in which only one polypeptide, TATA-binding protein (TBP) binds to the TATA box. TATA-binding protein binds specifically to the TATAA consensus sequence, and approximately 10 other polypeptides, called TBP-associated factors.
TATA-binding protein is a monomeric protein and plays a major role in transcription initiation. All eukaryotic TBPs analyzed have very highly conserved C-terminal domains of 180 residues. This conserved domain functions as well as the full-length protein in in vivo transcription. When TATA-binding protein (TBP) binds to a TATA box within the DNA, it inserts amino acid side chains between DNA base pairs, thus distorting the DNA. By inserting amino acid side chains between base pairs, TBP partially unwinds the helix and doubly kinks it. TBP binds with the negatively charged phosphates in the DNA backbone through positively charged lysine and arginine amino acid residues. The strain imposed on the DNA through this interaction initiates the melting, or separation, of the strands.
TFIIA
The general transcription factor TFIIA binds with the TBP subunit of TFIID, thus enhancing the binding between TFIID and the TATA box. Interaction of TFIIA with TBP facilitates the formation of the pre-initiation complex and its stabilization. The binding also results in the exclusion of negative (repressive) factors that might otherwise bind to TBP and interfere with the pre-initiation complex formation. The binding of TFIIA with TFIID prevents the binding of inhibitory factors. Thus, the formation of the transcription complex continues with the binding of other transcription factors.
Two separate genes encode TFIIA. One of the genes encodes a large subunit (TFIIAL, TOA1; gene name GTF2A1). The second one encodes a small subunit ( TFIIAS, TOA2; gene name GTF2A2). Both genes are present in species ranging from humans to yeast. Their protein products interact to form a complex composed of a beta-barrel domain and an alpha-helical bundle domain. It is the N-terminal and C-terminal regions of the large subunit that participate in interactions with the small subunit.
TFIIB
The binding of TFIID with the TATA box is followed by the binding of a transcription factor TFIIB. The transcription factor TFIIB binds to the TATA-binding protein (TBP) as well as to DNA sequences that are present upstream of the TATA box in some promoters. TFIIB makes protein-protein interactions with the TBP subunit of TFIID, and the RPB1 subunit of RNA polymerase II. TFIIB acts as a bridge in the binding of RNA polymerase II with the TBP-TFIIB complex in association with a third factor, TFIIF.
TFIIF
The RNA polymerase pre-initiation complex is formed by the binding of the transcription factor TFIIF. It binds to RNA polymerase II, which is not bound to any other transcription factor. Thus, it avoids contacting DNA outside the promoter. Furthermore, TFIIF stabilizes the RNA polymerase II while it’s contacting TBP and TFIIB.
TFIIE
The formation of RNA polymerase II pre-initiation complex needs the transcription factor TFIIE. Following the recruitment of RNA polymerase II to the promoter, two additional transcription factors, i.e., TFIIE and TFIIH are required for the initiation of transcription. TFIIE is thought to be involved in DNA melting at the promoter: it contains a zinc ribbon motif that can bind single-stranded DNA.
TFIIH
TFIIH is a multisubunit factor that plays two important roles in the formation of the RNA polymerase II transcription complex. Both helicase and kinase activities are ingrained inside it. The two subunits of TFIIH ( XPB and XPD proteins) are helicases, which unwind DNA around the initiation site. The subunit containing the protein kinase activity phosphorylates repeated sequences present in the C-terminal domain of the largest subunit of RNA polymerase II. The polymerase II C-terminal domain (CTD) consists of tandem repeats (27 repeats in yeast and 52 repeats in humans) of 7 amino acids with the consensus sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser.
Phosphorylation of these amino acids releases the polymerase from its association with the pre-initiation complex. It leads to the further recruitment of other proteins that allow the polymerase to initiate transcription and begin the synthesis of a growing mRNA chain. TFIIH, thus plays a vital role in the control of transcription elongation. Components of TFIIH (XPB and XPD proteins) are also required for DNA repair (nucleotide excision repair) and in phosphorylation of the cyclin-dependent kinase complexes regulating the cell cycle.
Promoters containing an initiator sequence (INR)
RNA polymerase transcribes many genes, whose promoters contain an initiator sequence (Inr) other than the TATA box. Some promoters contain only an Inr element but no TATA box. Many promoters lacking a TATA box, contain an Inr element and an additional downstream promoter element (DPE), located approximately 30 base pairs downstream of the transcription start site. It functions cooperatively with the Inr sequence. For initiation of transcription, the promoters having no TATA box require the transcription factor TFIID. TFIID binds to the Inr and DPE sequences through its other subunits (TAFs). The binding of TAFs to these elements recruits TBP to the promoter. The transcription factor TFIIB, polymerase II, and additional transcription factors are recruited gradually like that which occurs in TATA box promoters.
Transcription factors linked to RNA polymerase I and II
Transcription of ribosomal RNA genes, which are present in tandem repeats, is associated with RNA polymerase I. The promoter of ribosomal RNA genes spans about 150 base pairs just upstream of the transcription initiation site. Two transcription factors, UBF and SL1 recognize these promoter sequences. UBF and SL1 bind cooperatively to the promoter followed by recruitment of polymerase I to form an initiation complex.
UBF is a nucleolar phosphoprotein having both DNA binding and transactivation domains. The DNA-binding and transactivation domains of UBF overlap and dimerize through the amino-terminus, which is essential for the activation function of UBF. UBF activation requires the upstream control element (UCE; −156 to −107) of the rDNA promoter. SL1 functions through the essential core element (−45 to +18), overlapping the start site (+1) of transcription. UBF can interact with SL1, through its highly acidic carboxy-terminal domain as well as with Polymerase I (Pol I). UBF recruits SL1 and Pol I to the rDNA promoter, activating transcription by facilitating PIC (Pre-initiation complex) assembly.
The SL1 transcription factor
The SL1 transcription factor is composed of four protein subunits. TBP is a member of the four subunits. It is a common transcription factor required by all three classes of RNA polymerases. The association of TBP with ribosomal RNA genes is mediated by the binding of other proteins in the SL1 complex to the promoter. This is similar to the association of TBP with the Inr sequences of polymerase II genes that lack TATA boxes.
The SNAP complex
Promoters of the genes transcribed by RNA polymerase III, encoding small nuclear RNAs, are located upstream of the transcription start site. These promoters contain a TATA box along with a proximal sequence element (PSE). The proximal sequence element is recognized by a multi-subunit complex called the SNAP complex. Since the SNAP complex can bind to the PSE on its own, it corresponds to a sequence-specific DNA binding basal transcription factor. On a basal RNA polymerase III promoter, containing both a PSE and a TATA box, the SNAP complex binds cooperatively with TBP. This effect is dependent on the amino-terminal domain of TBP.
Conclusion
The process of synthesis of RNA from a DNA template is called transcription. It is the first step of gene expression. Here, a particular segment of DNA is copied into RNA by the enzyme RNA polymerase. The transcription process begins with binding the transcription factors with the enzyme RNA polymerase. Transcription begins with the binding of the transcription factors with the enzyme RNA polymerase.
The specific proteins required for RNA polymerase II to initiate transcription are called transcription factors. Transcription factors regulate gene expression alone or with other proteins in a complex. They promote the expression of genes as activators or block the recruitment of RNA polymerase to specific genes by acting as repressors. Two types of transcription factors have been defined i.e., general transcription factors and gene-specific transcription factors.
In eukaryotes, RNA polymerase II requires general transcription factors (GTFs) for initiation of transcription. The most common general transcription factors are TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH.
The enzyme polymerase II transcribes promoters of many genes containing a sequence TATAA. The sequence known as the TATA box, presents 25 to 30 nucleotides upstream of the transcription start site. The general transcription factor TFIID binds to the TATA box. The binding begins the first step in the formation of a transcription complex. The general transcription factor TFIIA binds with the TBP subunit of TFIID, thus enhancing the binding between TFIID and the TATA box. Interaction of TFIIA with TBP facilitates the formation of the pre-initiation complex and its stabilization. The transcription factor TFIIB binds to the TATA-binding protein (TBP) as well as to DNA sequences that are present upstream of the TATA box in some promoters. The formation of RNA polymerase II pre-initiation complex needs the transcription factor TFIIF, TFIIE, and TFIIH.
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I, Swagatika Sahu (author of this website), have done my master’s in Biotechnology. I have around twelve years of experience in writing and believe that writing is a great way to share knowledge. I hope the articles on the website will help users in enhancing their intellect in Biotechnology.