Def. one “of the simplest or essential parts or principles of which anything consists, or upon which the constitution or fundamental powers of anything are based”^[1] is called an element.

“S. cerevisiae promoters have multiple essential elements for the accurate transcriptional regulation of genes, including a core promoter region, an upstream activator sequence (UAS), an upstream repressor sequence (URS) and nucleosome-disfavoring sequences, such as poly(dA:dT) sequences […]. Each of these elements plays a vital role in tuning promoter activities, thus, it is important to understand the functions and combinatorial regulatory mechanisms of these elements to predict their functions. In order to obtain a comprehensive understanding of the promoter regulatory mechanisms, several tools have been developed, such as YEASTRACT (Yeast search for transcriptional regulators and consensus tracking) and SCPD (Saccharomyces cerevisiae promoter database) [18,19,20,21].”^[2]

“Type II restriction endonucleases recognize specific DNA sequences and cleave DNA at specified locations within or adjacent to their recognition sites, in reactions that normally require only Mg²⁺ as a cofactor (1–3). In many cases, the recognition sequence is a symmetrical palindrome of 4–8 consecutive base pairs, though some recognize discontinuous palindromes, interrupted by a segment of specified length but unspecified sequence (4,5). Many of the enzymes that act at palindromic sites are dimers that interact symmetrically with their targets, positioning one active site on each strand of the DNA: e.g. EcoRI, EcoRV and BamHI (6). They normally cut both strands within the lifetime of the enzyme–DNA complex (7–9). The phosphodiester bonds cleaved by these enzymes are usually located within the sequence: in some cases, near the 5′ ends, to leave duplexes with 5′ single-strand extensions; in others, at the middle of the site, to leave flush-ended duplexes; in further cases, near the 3′ ends. However, a subset of the Type II systems, called Type IIS (5), recognize asymmetric sequences and cleave both strands at specific locations on one side of the recognition site. Another subset, the Type IIB enzymes, also cut the DNA at specified positions distant from their recognition sites, but on both sides of the sequence.”^[3]

Angiotensinogen core promoter element 1 (AGCE1) is an example of a core promoter element that may occur in a DNA sequence for only one gene (the human angiotensinogen gene angiotensin).

The core promoter element X core promoter element 1 (XCPE1) directs activator-, mediator-, protein-dependent but TFIID-independent RNA polymerase II transcription from TATA box-less promoters.^[4]

This promoter element appears to be exclusively human such as the group in the image at the right.

Metal responsive elements (MRE)s, or TGC boxes, may occur in the core promoter of some human DNA genes.

Notation: let the symbol MT stand for metallothionein.

“The metallothionein (MT) genes provide a good example of eucaryotic promoter architecture. MT genes specify the synthesis of low-molecular-weight metal-binding proteins. They are transcriptionally regulated by the metal ions cadmium and zinc (11), glucocorticoid hormones (18), interferon (14), interleukin-1 (22), and tumor promoters (2). The metal ion regulation of MTs is conferred by a short sequence element called the metal-responsive element (MRE [21]) or TGC box (31, 34), which functions as a metal ion-dependent enhancer.”^[5]

“cAMP-response-element modulator (CREM), a transcription factor responsive to the cAMP signal transduction pathway, drives expression of key testis-specific genes.”^[6]

“Transcription factors of the cAMP-response-element binding protein (CREB)–CREM family target genes with cAMP response elements (CREs) constituted by the palindromic consensus sequence TGACGTCA (Sassone-Corsi et al. 1988).”^[6]

“Within the activation domain is the P-(phosphorylation) box containing the target residue for PKA phosphorylation, among other phosphoacceptor sites.”^[6]

The EIF4E basal element, also eIF4E, (4EBE) is a basal promoter element for the eukaryotic translation initiation factor 4E. “Interactions between 4EBE and upstream activator sites are position, distance, and sequence dependent.”^[7]

The GAAC element is usually a core promoter element containing guanine (G), adenine (A), and cytosine (C), “able to direct a new transcription start site 2-7 bases downstream of itself, independent of TATA and Inr regions.”^[8]

The motif ten element (MTE) “promotes transcription by RNA polymerase II when it is located precisely at positions +18 to +27 relative to A₊₁ in the initiator (Inr) element.”^[9]

“The B recognition element (BRE) is a DNA sequence found in the promoter region of most genes in eukaryotes and Archaea.^[10][11]“^[12]

“The BRE is a cis-regulatory element that is found immediately upstream of the TATA box, and consists of 7 nucleotides.”^[12]

In the archaean from the Dead Sea imaged at the right, “We have completely fragmented their DNA. I mean we have completely destroyed it by bombarding it with [radiation]. And they can reassemble their entire chromosome and put it back into working order within several hours.”^[13]

The downstream B recognition element designated as the BRE^d,^[14] or dBRE, is an additional core promoter element that occurs downstream of the TATA box and is recognized by general transcription factor II B.^[14]

In the biosynthesis of any human protein, the gene that contains the nucleotide sequence which is translated into that protein must be transcribed. For RNA polymerase II holoenzyme to transcribe the gene, the gene’s promoter must be located. After the promoter is located, the transcription start site (TSS) is pinpointed by using nucleotide sequences that include the TSS. Within the promoter, most human genes lack a TATA box and have an initiator element (Inr) or downstream promoter element instead.

The downstream core element (DCE) is a transcription core promoter sequence that is within the transcribed portion of a gene.

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.^[15]

“The downstream promoter element (DPE) is a core promoter element … present in other species including humans and excluding Saccharomyces cerevisiae.^[16]“^[17]

“Like all core promoters, the DPE plays an important role in the initiation of gene transcription by RNA polymerase II.”^[17]

1. No gene transcription element is used to transcribe A1BG.

The content on this page was first contributed by: Henry A. Hoff.

Initial content for this page in some instances came from Wikiversity.