# Gene transcriptions/General factors/II Ds

The general transcription factor II D (TF$_{II}$D) is one of several general transcription factors that make up the RNA polymerase II preinitiation complex. Before the start of transcription, the transcription factor II D (TFIID) complex, binds to the core promoter of the gene.
TFIID is the first protein to bind to DNA during the formation of the pre-initiation transcription complex of RNA polymerase II (RNA Pol II). Binding of TFIID to the TATA box in the promoter region of the gene initiates the recruitment of other factors required for RNA Pol II to begin transcription. Some of the other recruited transcription factors include TFIIA, TFIIB, and TFIIF. Each of these transcription factors is formed from the interaction of many protein subunits, indicating that transcription is a heavily regulated process.
"Several of the TFIID subunits have been implicated in core promoter selectivity (Verrijzer and Tijan, 1996; Hampsey and Reinberg, 1997; Smale, 1997; Hahn, 1998)."

## Genetics

Genetics involves the expression, transmission, and variation of inherited characteristics.

## Gene transcriptions

DNA is a double helix of interlinked nucleotides surrounded by an epigenome. On the basis of biochemical signals, an enzyme, specifically a ribonucleic acid (RNA) polymerase, is chemically bonded to one of the strands (the template strand, usually) of this double helix. The polymerase, once phosphorylated, begins to catalyze the formation of RNA using the template strand. Although the catalysis may have more than one beginning nucleotide (a start site) and more than one ending nucleotide (a stop site) along the DNA, each nucleotide sequence catalyzed that ultimately produces approximately the same RNA is part of a gene. The catalysis of each RNA representation from the template DNA is a transcription, specifically a gene transcription. The overall process is also referred to as gene transcription.

## General transcription factors

General transcription factors (GTFs), also known as basal transcriptional factors, are a class of protein transcription factors that bind to specific sites on DNA to activate transcription. GTFs, RNA polymerase, and the mediator multiple protein complex constitute the basic transcriptional apparatus.

## Phosphates

"The amount of phosphate needed or available for a purpose, including estimates of phosphate in and phosphate out, and the phosphate form, determine the phosphate budget for a cell or an entire organism." Bold added. For a "standard man" of 70 kg the available phosphate is ~1.52 x 10$^{25}$ molecules of phosphate in some form. The available phosphate of an adult human female may differ from the "standard man".

## Core promoters

The core promoter is the minimal portion of the promoter required to properly initiate gene transcription.
It contains a binding site for RNA polymerase (RNA polymerase I, RNA polymerase II, or RNA polymerase III) holoenzymes.
A vast network of regulatory factors that contribute to the initiation of transcription by RNA polymerase ultimately target any specific gene’s core promoter.
The core promoter includes the transcription start site(s) (TSS).
That portion of the core promoter that is upstream of the TSS is also part of the proximal promoter.
The core promoter is approximately -34 bp upstream from the TSS.
"Several factors have been identified that bind to core promoters (reviewed in Smale, 1997)".
TFIID binds to the core promoter to position the polymerase properly.

## TATA boxes

"The TATA box (also named the Goldberg-Hogness box after its discoverers) [is] the first core promoter element identified in eukaryotic protein-coding genes." Bold added. It "is a cis-regulatory element" found in the promoter region of genes in archaea and eukaryotes. "About 24% of human genes have a TATA-like element and their promoters are generally AT-rich".

## TATA binding proteins

The TATA-binding protein (TBP) is a general transcription factor that binds specifically to a DNA sequence called the TATA box. This DNA sequence is found about 25 base pairs upstream of the transcription start site in some eukaryotic gene promoters.
TBP is involved in DNA melting (double strand separation) by bending the DNA by 80° (the AT-rich sequence to which it binds facilitates easy melting). The TBP is an unusual protein in that it binds the minor groove using a β sheet.
TBP is also a necessary component of RNA polymerase I and RNA polymerase III, and is, it is thought, the only common subunit required by all three of the RNA polymerases.

## TATA binding protein associated factors

When there is no TATA box nucleotide sequence in the gene promoter region of the DNA next to a gene, a TATA binding protein associated factor (TAF) will bind sequence specifically and force the TATA box binding protein to bind non-sequence specifically to the DNA in the promoter region.
"[T]he TAFs contribute to basal activities on non-TATA core elements in the context of TATA-less as well as TATA-containing promoters (Kaufmann and Smale, 1994; Martinez et al., 1994; Verrijzer et al., 1994, 1995; Burke and Kadonaga, 1996, 1997)."
"TAF-independent TATA-less transcription has also been described (Aso et al., 1994; Weis and Reinberg, 1997)."
The TAFs or alternates that compose the general transcription factor II D are TAF1 - TAF4, TAF4B, TAF5 - TAF9, TAF9B, TAF10 - TAF13, and TAF 15.

## Complex assembly

TFIID serves as the scaffold for assembly of the remainder of the transcription complex.

## Transcription initiations

TFIID coordinates the activities of more than 70 polypeptides required for initiation of transcription by RNA polymerase II.