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https://en.wikipedia.org/wiki/Transcription_factor

_____ Mechanism[edit source] Transcription factors bind promoter regions or intronic sequence of the genes that they regulate

Transcription factors bind to either enhancer or promoter regions of DNA adjacent to the genes that they regulate, or intronic sequences within a given locus. Depending on the transcription factor, the transcription of the target gene can be either up- or down-regulated. Transcription factors use a range of mechanisms to regulate gene expression[12], including:

- Stabilize or block the binding of DNA-dependent RNA polymerase to DNA. - Catalyze chemical modification(s) of specific amino acids within histone subunits. Examples include the addition or removal of acetyl groups (known as histone acetylation and deacetylation, respectively). This can be directed by the transcription factor itself (if such an enzymatic domain is present), or by recruiting additional proteins Transcription factor can do this either directly (if such an enzymatic domain is present) or recruit additional proteins with this catalytic activity. Many transcription factors use one or the other of two opposing mechanisms to regulate transcription:[13] - histone acetyltransferase (HAT) activity – acetylates histone proteins, which weakens the association of DNA wrapped around histones, which make the DNA more accessible to transcriptional machinery (DNA-dependent RNA polymerases), thereby up-regulating transcription. - histone deacetylase (HDAC) activity – deacetylates histone proteins, which strengthens the association of DNA with histones, which make the DNA less accessible to transcription, thereby down-regulating transcription - recruit coactivator or corepressor proteins to the transcription factor DNA complex[14]

In plants, much work has been carried out to elucidate the mechanism by which transcription factors with repression domains carry out their function. EAR containing proteins such as AP2 recruit TOPLESS which in turn recruits the histone deacetylase.

AGAMOUS intron 2

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Transcription factors are modular in structure and contain the following domains:[1]

DNA-binding domain (DBD), which bind DNA in a sequence-specific manner. Transcription factors may bind promoters and intronic sequences).

(enhancer or promoter. Necessary component for all vectors. Used to drive transcription of the vector's transgene promoter sequences) adjacent to regulated genes. DNA sequences that bind transcription factors are often referred to as response elements.

Trans-activating domain (TAD), which contains binding sites for other proteins such as transcription coregulators. These binding sites are frequently referred to as activation functions (AFs).[41]

Repression domain (RD). Repression domains are often surfaces for protein-protein interaction, allowing for the recruitment of co-repressors or histone modifiers. In Arabidopsis, one such co-repressor is TOPLESS, which binds EAR domains.

An optional signal sensing domain (SSD) (e.g., a ligand binding domain), which 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. Also, the DBD and signal-sensing domains may reside on separate proteins that associate within the transcription complex to regulate gene expression. Trans-activating domain[edit source] Main article: Trans-activating domain TAD is domain of the transcription factor that binds other proteins such as transcription coregulators. Proteins containing TADs are Gal4, Gcn4, Oaf1, Leu3, Rtg3, Pho4, Gln3 in yeast and p53, NFAT, NF-κB and VP16 in mammals.[42] Many TADs are as short as 9 amino acids (present in e.g., p53, VP16, MLL, E2A, HSF1, NF-IL6, NFAT1 and NF-κB Gal4, Pdr1, Oaf1, Gcn4, VP16, Pho4, Msn2, Ino2 and P201).