In molecular biology, a transcription factor is a protein that binds DNA at a specific promoter or enhancer region or site, where it regulates transcription. Transcription factors can be selectively activated or deactivated by other proteins, often as the final step in signal transduction. Molecular biology is the study of biology at a molecular level. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... The general structure of a section of DNA Deoxyribonucleic acid (DNA) is a nucleic acid —usually in the form of a double helix— that contains the genetic instructions specifying the biological development of all cellular forms of life, and most viruses. ... In genetics, a promoter is a DNA sequence that enables a gene to be transcribed. ... In genetics, an enhancer is a short region of DNA that can be bound with proteins (namely, the trans-acting factors, much like a set of transcription factors) to enhance transcription levels of genes (hence the name) in a gene-cluster. ... Transcription is the process through which a DNA sequence is enzymatically copied by an RNA polymerase to produce a complementary RNA. Or, in other words, the transfer of genetic information from DNA into RNA. In the case of protein-encoding DNA, transcription is the beginning of the process that ultimately... It has been suggested that cell signaling be merged into this article or section. ...

Classes

There are three classes of transcription factors:

• General transcription factors are involved in the formation of a preinitiation complex. The most common are abbreviated as TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH. They are ubiquitous and interact with the core promoter region surrounding the transcription start site(s) of all class II genes.
• Upstream transcription factors are proteins that bind somewhere upstream of the initiation site to stimulate or repress transcription.
• Inducible transcription factors are similar to upstream transcription factors but require activation or inhibition.

General Definition- Protein required for recognition by RNA polymerases of specific stimulatory sequences in eukaryotic genes. General transcription factors (GTFs) are proteins which have been shown to be important in the transcription of class II genes to mRNA templates. ... A preinitiation complex (abbreiviated PIC) is an ordered combination of six general transcription factors: TFIIA TFIIB TFIID TFIIE TFIIF TFIIH The preinitiation complex combines with RNAP near the transcriptional start site, to support a basal level of transcription. ... A class II gene is a type of gene that codes for a protein. ... In molecular biology, an upstream transcription factor is a protein which binds to a cis-regulatory element (such as an enhancer or repressor sequence) upstream from a gene and either directly or indirectly affects the initiation of transcription. ...

Motifs found in transcription factors

• Helix-turn-helix (HTH) bind the major groove of the DNA.
• Zinc fingers function as structural platforms for DNA binding.
• Leucine zippers function in associating the transcription factors with each other.
• Basic-helix-loop-helix (bHLH) bind DNA with two alpha helices containing basic amino acid residues which are linked by a loop and are typically dimeric.
• G-quadruplex Motifs are recently being studied extensively for their role as a TF binding site

The λ repressor of bacteriophage lambda employs a helix-turn-helix to bind DNA. In proteins, the helix-turn-helix (HTH) is a major structural motif capable of binding DNA. It is composed of two α helices joined by a short strand of amino acids and is found in many... A zinc finger is part of a protein that can bind to DNA. Zinc finger domains typically consist of two antiparallel β sheets, each carrying a cysteine residue, and an α helix carrying two histidine residues. ... This article needs to be cleaned up to conform to a higher standard of quality. ... Why doesnt this site have bhlh on it? its got really dumb sites but none about bhlh or hlh. ... A diagram of the alpha helix structure of amino acids In proteins, the α helix is a major structural motif in secondary structure. ... An amino acid residue is what is left of an amino acid once a molecule of water has been lost (an H+ from the nitrogenous side and an OH- from the carboxylic side) in the formation of a peptide bond. ... Sucrose, or common table sugar, is composed of glucose and fructose. ... G-quadruplex or G4 DNA is well known as DNA structural motifs that cap eukaryotic chromosomal ends (telomeres). ...

Examples of transcription factors

STAT

The Signal Transducers and Activator of Transcription (STAT) protein regulate many aspects of cell growth, survival and differentiation. The transcription factors of this family are activated by the Janus Kinase JAK and dysregulation of this pathway is frequently observed in primary tumors and leads to increased angiogenesis and enhanced survival of tumors. Knockout studies have provided evidence that STAT proteins are involved in the development and function of the immune system and play a role in maintaining immune tolerance and tumor surveillance. The Signal Transducers and Activator of Transcription (STAT) protein regulates many aspects of cell growth, survival and differentiation. ... This article needs to be wikified. ... Angiogenesis is the physiological process involving the growth of new blood vessels from pre-existing vessels. ... Knockout (also referred to as a K.O. or knock), is a winning criterion in several full-contact combat sports, such as Boxing, Kickboxing, Muay Thai and others sports involving striking. ...

Function of STAT proteins

STAT proteins were originally described as latent cytoplasmic transcription factors that require phosphorylation for nuclear retention. The unphosphorylated STAT proteins shuttle between the cytosol and the nucleus waiting for its activation signal. Once the activated transcription factors reach the nucleus, they bind to a consensus DNA-recognition motif called gamma activated sites (GAS) in the promoter region of cytokine-inducible genes and activate transcription of these genes. Cytoplasm is like jelly-like material that fills cells. ... Phosphorylation is the addition of a phosphate (PO4) group to a protein or a small molecule. ... ÃThe cytosol (as opposed fatty cytoplasm, which also includes the organelles) is the internal fluid of the cell, and a large part of cell metabolism occurs here. ... In genetics, a promoter is a DNA sequence that enables a gene to be transcribed. ... Cytokines are small protein molecules that regulate communication among immune system cells and between immune cells and those of other tissue types. ...

Activation of STAT proteins

Extracellular binding of Cytokines induces activation of the intracellular Janus kinase that phosphorylates a specific tyrosine residue in the STAT protein which promotes the dimerization of STAT monomers via their SH2 domain. The phosphorylated dimer is then actively transported in the nucleus via importin a/b and RanGDP complex. Once inside the nucleus the active STAT dimer binds to cytokine inducible promoter regions of genes containing gamma activated site (GAS) motif and activate transcription of this proteins. The STAT protein can be dephosphorylated by nuclear phosphatases which leads to inactivation of STAT and the transcription factor becomes transported out of the nucleus by exportin crm1/RanGTP.gg Cytokines are small protein molecules that regulate communication among immune system cells and between immune cells and those of other tissue types. ... Ribbon diagram of the SH2 domain of human P56-Lck tyrosine kinase (PDB accession code 1LKK, chain A), colored from blue (N-terminus) to red (C-terminus). ... A phosphatase is an enzyme that hydrolyses phosphoric acid monoesters into a phosphate ion and a molecule with a free hydroxy group. ...

See also

• DNA-binding protein
• E2F
• Oct-4
• Nanog (transcription factor)
• Brachyury
• Pax genes
• Sox2

DNA-binding proteins are a broad class of protein molecules that possess certain structural motifs (e. ... E2F stands for family of transcription factors (TF) in higher eukaryotes. ... Oct-4 is an abbreviation of Octamer-4. ... Nanog (pron. ... The brachyury mutation was first described in mice in 1927 as a mutation that affected the tail length in heterozygous animals and was lethal in homozygous animals due to defects in notochord differentiation and the abscence of structures posterior to the forlimb bud. ... // Introduction Paired box (Pax) genes are a family of tissue specific transcription factors containing a PAIRED domain and usually a partial or complete homeodomain. ... Sox2 is a transcription factor that is essential to maintain self-renewal of undifferentiated embryonic stem cells. ...

External links

• A classification of transcription factors based on their DNA-binding domains

• Stat constructs from James Darnell lab

Entries of transcription factors at genetic databases

• TFIIA
• TFIIB
• TFIID
• TFIIE
• TFIIF
• TFIIH