Transcription, generally

In eukaryotes, general transcription factors must bind to the promoter to allow RNA polymerase II to bind and form the initiation complex at the start site for transcription. General manscription factors are common to most genes. The general transcription factor TFIID (the TATA fector) must bind to the TATA box before RNA polymerase II can bind. Other examples delude SP-1 and NF-.l that modulate basal transcription of many genes. 

Transcriptional activators can intervene as regulators at various steps in the initiation of transcription. They can interact with components of TFIID, as well as with components of RNA polymerase II, to stimulate transcription. Regulated transcription generally requires the aid of further protein components, which are commonly termed coactivators (see 1.4.3.2). An understanding of the details of coactivator function is only just emerging. 

The general transcription factor TFllD is believed to be the key link between specific transcription factors and the general preinitiation complex. However, the purification and molecular characterization of TFllD from higher eucaryotes have been hampered by its instability and heterogeneity. All preparations of TFllD contain the TATA box-binding protein in combination with a variety of different proteins called TBP-associated factors, TAFs. When the preinitiation complex has been assembled, strand separation of the DNA duplex occurs at the transcription start site, and RNA polymerase II is released from the promoter to initiate transcription. However, TFIID can remain bound to the core promoter and support rapid reinitiation of transcription by recruiting another molecule of RNA polymerase. 

Another obvious advantage that the LG method typically enjoys over floating-point methods is one of programming efficiency. Because LG dynamics are a natural transcription of the kinetic processes taking place on the micro-lattice, the actual program code is generally concise and straightforward, and often amounts to little more than a few dozen lines of FORTRAN. 

The antagonist-induced conformation of nuclear hormone receptors attracts co-repressors like Nco/SMRT (nuclear hormone receptor co-repressor/silencing mediator of retinoid and thyroid receptors) which further recruit other nuclear proteins with histone deacetylase activity. Their action leads to chromatin condensation, thus preventing the general transcription apparatus from binding to promoter regions. 

DNA response elements are generally found a short distance upstream of promoters in selected genes. They are specific for selective transcription factors and... 

General or basic transcription factors are required for every gene to allow the proper recruitment of RNA polymerases to ensure transcriptional activity. They bind to core promoters in the vicinity of transcriptional start sites in a sequential manner. 

A leucine zipper is a structural motif present in a large class of transcription factors. These dimeric proteins contain two extended alpha helices that grip the DNA molecule much like a pair of scissors at adjacent major grooves. The coiled-coil dimerization domain contains precisely spaced leucine residues which are required for the interaction of the two monomers. Some DNA-binding proteins with this general motif contain other hydrophobic amino acids in these positions hence, this structural motif is generally called a basic zipper. 

Nuclear Receptor Regulation of Hepatic Cytochrome P450 Enzymes. Figure 1 General mechanism for transcriptional activation of CYP genes by xenochemicals that activate their cognate xeno-receptor proteins. In the case of Ah receptor, the receptor s heterodimerization partner is Arnt, whereas in the case of the nuclear receptors CAR, PXR, and PPARa, the heterodimerization partner is RXR. The coactivator and basal transcription factor complexes shown are each comprised of a large number of protein components. 

Figure 3 provides a very general overview of transcriptional activation in response to a PPAR ligand. Fig. 3a shows the schematic representation of a PPAR target gene in the absence of PPAR ligand. Co-repressor proteins bound to both unliganded PPAR and RXR... 

The multiprotein unit that synthesize RNA by copying the sequence information from the leading strand of the DNA. Its activity is tightly controlled by phosphorylation of the C-termal domain (CTD), access to DNA and interaction by general and sequence specific transcription factors and coactivators and corepressors. 

Proteins that bind DNA at specific DNA sequences often distal from transcriptional start sites of genes. Their binding and activity is usually cell type or stimulus triggered, which subsequently decondensate the chromatin and finally lead to the recruitment of general transcription factors and the RNA polymerase. 

Consensus sequence in the promoter region of many eukaryotic genes that bind a general transcription factor and hence specifies the position where transcription is initiated by the RNA polymerase. 

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