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Overview of transcription factors

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INTRODUCTION — Transcription is the process whereby the information in genomic DNA is transferred to RNA. The transcription of all genes requires the activity of critical core components that initiate the construction and elongation of RNA. Elements of this basic machinery include the transcription initiation complex and various transcription factors.
The transcription initiation complex consists of multiple molecules, including RNA polymerase II and the TATA binding factor. Most, but not all, genes have a TATA box located approximately 20 and 30 base pairs upstream of the transcription initiation site. This element helps specify the precise site at which transcription is initiated by binding the TATA binding factor. The exact sequence of the TATA box is variable. A number of related thymine and adenine rich sequences all confer TATA box function.
Transcription also requires various additional proteins, named transcription factors, that bind to specific recognition sequences close to the transcription initiation sites. This binding provides a mechanism for tissue- and stimulus-specific gene expression: Tissue-specificity is determined in part by the profile of transcription factors expressed in a given cell type. Stimulus-specificity is partly based upon the occupancy and activation of particular receptors, which leads to transcription factor-mediated alterations in gene expression.
Hundreds of transcription factors have been identified. These factors and their recognition elements are listed on several websites, including TRANSFAC, JASPAR, and TELIS [1-4]. These websites organize transcription factors based upon the presence of specific motifs, such as the following: Leucine zippers (eg, a sequence consisting of a leucine residue at every seventh position) Zinc fingers (eg, the presence of a number of residues – usually four cysteine molecules – that coordinate one zinc ion) Helix-loop-helix (eg, two potential alpha helices connected by a loop of variable length)
Alternatively, the proteins can be characterized based on DNA binding motifs and some databases allow searches based on user-specified features.
An encyclopedic compendium of transcription factors is beyond the scope of this topic review. Instead, the general properties of transcription factors will be presented, followed by a brief review of the specific characteristics of a few, and the consequences of mutations in transcription factors. A review of the basics of molecular biology is presented separately. (See “Overview of molecular biology”).
OVERVIEW OF TRANSCRIPTION FACTOR FUNCTION
Properties — Certain characteristics are shared by nearly all transcription factors: All transcription factors bind to short recognition sequences within DNA and interact with the proteins of the transcription machinery. All transcription factors modulate the rate at which their target genes are transcribed. Recent work has demonstrated that the genome contains fewer genes than previously believed and that many genes encode multiple alternative transcripts. Parallel work in stem cell biology and tissue regeneration have revealed the existence of molecular switches that serve to drive cells along various developmental trajectories. These discoveries highlight the importance of transcription factor function in determining cell fate and establishing differentiated expression patterns. Transcription factors may be present in an inactive or active form. In the case of the nuclear hormone receptors, activation occurs after ligand binding. With other transcription factors, such as the signal transduction and activation of transcription proteins (STATs), protein phosphorylation causes activation. Other transcription factors are constitutively active. As an example, Pit-1 is always active, although it is synthesized only in the pituitary gland, presumably as a result of control by other transcription factors [2].
Functions — A cell’s developmental fate is a direct consequence of the specific receptors and transcription factors present within the cell when it is exposed to biologically active ligands. An enormous complexity of gene expression results from the combined actions of multiple ligands and receptors triggering downstream signaling via a large array of transcription factors.
The precise mechanisms by which transcription factors help regulate gene expression are not entirely known. A simplified view of this process is shown in the figure (show figure 1): The transcription factor binds to specific sites in the genome via its DNA binding domain. The transcription factor interacts (through additional domains) with other proteins that comprise the transcription initiation complex. The protein-protein interaction between the transcription factor and the initiation complex changes the activity of the initiation complex, resulting in a modification of the rate of transcription.
Assays of function — A commonly used in vitro method to detect the binding of transcription factors to their DNA recognition sites is the “electrophoretic mobility shift assay” or “electrophoretic gel retardation assay” (show figure 2). This assay exploits the property that a DNA-transcription factor protein complex and DNA alone migrate differently on a separating gel matrix, thereby causing a shift or retardation in movement.
The electrophoretic mobility shift assay is used to understand the following properties of transcription factors: What sequences are essential for transcription factor binding Where transcription factor recognition sites are located within specific genes What transcription factors bind to specific recognition sites
TRANSCRIPTION FACTOR MUTATIONS IN DISEASE — Mutations in specific transcription factors can lead to human disease and provide insight into the multi-faceted impact of these proteins. Examples include the transcription factors Runx2 and peroxisome proliferator-activated receptor gamma (PPARg).
Osteoblasts and adipocytes arise from a common precursor found in the bone marrow [5]. To illustrate the role of transcription factors in driving differentiation, this section will briefly review the roles of Runx2 and PPARg in driving the osteoblastic and adipocytic programs, respectively.
Cleidocranial dysplasia — Cleidocranial dysplasia was recognized as a clinical syndrome long before RUNX2 (also called OSF2 and CBFA1) was recognized as the gene mutated in the disorder. The cardinal clinical features of this disorder include delayed closure of cranial sutures, delayed tooth eruption, hypoplastic clavicles, short stature, scoliosis, and multiple additional skeletal abnormalities. Cleidocranial dysplasia is caused by a mutation in RUNX2, a member of the Runx family of transcription factors, located on chromosome 6p21. This single gene is responsible for the initial differentiation of osteoblasts to form skeletal structures [6,7]. (See “Normal skeletal development and regulation of bone formation and resorption”).
Linkage mapping revealed heterozygous deletions including the RUNX2 locus in affected families, and sequencing revealed various loss-of-function mutations in additional disease kindreds [7]. A mouse Runx2 knockout leads to features reminiscent of human cleidocranial dysplasia when heterozygous, and lethality at birth when homozygous, with global ossification failure [8]. Both intramembranous and endochondral ossification are disrupted, and mature osteoblastic protein products are not present in the matrix. These findings show that Runx2 serves as a key developmental switch in the osteoblastic lineage.
Runx2 also impacts maturation of the osteoclast and chondrocyte lineages. Osteoclast development requires signals provided by both macrophage colony stimulating factor (M-CSF) and receptor activator of NFkappaB ligand (RANKL), the latter produced by osteoblasts. Osteoclast development is impaired in the Runx2 knockout, while in vitro osteoblast-osteoclast co-culture experiments with Runx2 overexpressing cells show increased RANKL expression and enhanced osteoclastogenesis [8,9]. T
he effects on osteoclastogenesis show that Rankl is expressed early in the differentiation of the osteoblastic lineage, upstream of another “master” osteoblastic developmental switch, the transcription factor Sp7 (also known as Osterix). Sp7 knockout mice express Runx2, display global failure of skeletal development, but without impairment of osteoclast development [10]. Thus, while Runx2 gene expression is needed for osteoclastogenesis, Sp7 expression is not.
Indian hedgehog (IHH), a paracrine factor that regulates chondrocyte maturation in the growth plate, is also dependent on Runx2. In the absence of Runx2, IHH signaling is diminished, resulting in more rapid chondrocyte maturation and correspondingly decreased chondrocyte proliferation [11]. The cross-talk between Runx2 and IHH accounts for the shortened limb phenotype encountered in cleidocranial dysplasia.
Mutations in the PPAR gamma gene — PPARg is a member of the steroid hormone receptor superfamily and is active as a heterodimer with RXR. This receptor modulates a variety of interrelated processes, including adipogenesis (tontonoz cell 94), insulin sensitivity, lipid peroxidation, lipoprotein transport, and inflammatory cytokine release. It is the target of the currently used thiazolidinedione drugs rosiglitazone and pioglitazone, which act as PPARg agonists [12].
Two isoforms of PPARg are known, PPARg1 and PPARg2. PPARg2 includes an additional 28 N-terminal amino acid residue and is restricted in its expression to the adipocyte lineage [13]. Moreover, this isoform causes increased ligand-independent transcriptional activation [14]. In spite of a decade of intensive study, the natural ligands for PPARg remain incompletely known. Among the potential physiological ligands are 15-deoxy-D12,14 prostaglandin J2, the first identified ligand, an unidentified ligand induced during adipogenesis, and dietary lipids [15-18]. Importantly, PPARg can modulate transcription both in the presence and absence of bound ligand via its interactions with associated coactivator and corepressor proteins. In adipose tissue, PPARg leads to lipid trapping and promotion of the adipocytic differentiation program [19,20]. In liver, macrophages, and other tissues PPARg activation leads to lipid oxidation.
Thiazolidinedione drugs are potent PPARg agonists [21]. Their therapeutic actions include increasing peripheral glucose disposal, leading to marked improvement in insulin sensitivity [22]. The improvement in insulin sensitivity is accompanied by an increase in the mass of adipose tissue and, in a sizable fraction of patients, by fluid retention. As noted above, both adipocytes and osteoblasts arise from a common precursor cell. Given the role of thiazolidinediones in promoting the adipocytic developmental program, it is not surprising that reduced bone formation has been observed in response to the drugs’ administration in animal models [23-25]. However, whether similar adverse effects on bone mass occur in humans remains an open question [26,27].
Rare individuals have been reported with dominant-negative PPARg gene mutations. These patients manifest a syndrome that combines lipodystrophy with features of the metabolic syndrome, including insulin resistance, type 2 diabetes, hepatic steatosis, dyslipidemia, hypertension, and polycystic ovary syndrome in women [28-30]. A common P12A polymorphism is associated with type 2 diabetes risk, with the proline allele conferring a relative risk of 1.25 compared to the alanine allele [31]. (See “The metabolic syndrome (insulin resistance syndrome or syndrome X)”).
SUMMARY — Transcription factors serve as molecular switches that allow modulation of gene expression and enable a multiplicity of cellular phenotypes to be generated from a limited number of genes. They are critical to both cellular development and responsiveness to physiological and pathological stimuli. Mutations in transcription factors have been identified as causes of syndromic human diseases.

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