# Gene transcriptions/Elements/Downstream promoters

The figure on the right is an overview of four core promoter elements: the B recognition element (BRE), TATA box, initiator element (Inr), and downstream promoter element (DPE), showing their respective consensus sequences and their distance from the transcription start site.
"The downstream promoter element (DPE) is a core promoter element ... present in other species including humans and excluding Saccharomyces cerevisiae."
"Like all core promoters, the DPE plays an important role in the initiation of gene transcription by RNA polymerase II."

## Gene transcriptions

"Transcription by RNA polymerase II is directed by cis-acting [close-acting] DNA sequences that typically consist of a core promoter along with regulatory elements, such as enhancers [trans-acting, or distant-acting, protein factors], that contain binding sites for sequence-specific transcriptional activator and/or repressor proteins."

## Core promoters

"[T]he core promoter [consists of] the DNA sequences, which encompass the transcription start site (within about -40 and +40 [nucleotides] relative to the +1 start site".
"[T]he core sequence of the DPE is located at precisely +28 to +32 relative to the A$_{+1}$ nucleotide in the Inr". It is located about 28–33 nucleotides downstream of the transcription start site.
"DPE-dependent basal transcription depends highly on the Inr (and vice versa) and on correct spacing between the two elements."

## Initiator elements

"There is a strict requirement for spacing between the [Initiator element] Inr and DPE motifs, as an increase or decrease of 3 nucleotides in the distance between the Inr and DPE causes a seven- to eightfold reduction in transcription as well as a significant reduction in the binding of purified TFIID."

## Consensus sequences

"The DPE consensus sequence was originally thought to be RGWCGTG, however more recent studies have suggested it to be the similar but more general sequence RGWYV(T). In nucleic acid notation for DNA, R (puRine) stands for A/G (adenine or guanine, which are both purines); W (Weak) stands for A/T (adenine or thymine, which both form only two hydrogen bonds); Y (pYrimidine) stands for C/T (cytosine or thymine, which are both pyrimidines); and V stands for A/C/G."

## DPE-containing promoters

"The ... Drosophila Antennapedia P2 (Antp P2) [promoter contains] a 7-nucleotide sequence that conforms to the DPE consensus". GeneID: 40835 Antp Antennapedia [Drosophila melanogaster] is also known as Antp P2. GeneID: 3204 HOXA7 homeobox A7 [ Homo sapiens ] is also known as ANTP and "[t]his gene is highly similar to the antennapedia (Antp) gene of Drosophila." As GeneID: 3204 is " highly similar to the antennapedia (Antp) gene of Drosophila", it may have a DPE like the Drosophila gene core promoter does.
"[T]he TATA-less Drosophila Abdominal-B (Abd-B) promoter [has a] partial DPE sequence". GeneID: 3205 HOXA9 homeobox A9 [ Homo sapiens] is also known as ABD-B and "[t]his gene is highly similar to the abdominal-B (Abd-B) gene of Drosophila." GeneID: 3205 may also be TATA-less and have a DPE.

## General transcription factor II Ds

The DPE "is required for the binding of purified [general transcription factor II D] TFIID to a subset of TATA-less promoters".
"Photo-cross-linking analysis of purified TFIID with a TATA-less DPE-containing promoter revealed specific cross-linking of dTAFII60 [TAF6 GeneID: 6878] and dTAFII40 [TAF11 GeneID: 6882] to the DPE, with a higher efficiency of cross-linking to dTAFII60 than to dTAFII40. These data, combined with the previously well-characterized interactions between the two TAFs and their homology to histones H4 and H3, suggest that a dTAFII60–dTAFII40 heterotetramer binds to the DPE."

## Hypotheses

* The DPE is not used to transcribe A1BG.