E-box

An E-box (enhancer box) is a DNA response element found in some eukaryotes that acts as a protein-binding site and has been found to regulate gene expression in neurons, muscles, and other tissues. Its specific DNA sequence, CANNTG (where N can be any nucleotide), with a palindromic canonical sequence of CACGTG, is recognized and bound by transcription factors to initiate gene transcription. Once the transcription factors bind to the promoters through the E-box, other enzymes can bind to the promoter and facilitate transcription from DNA to mRNA. An E-box (enhancer box) is a DNA response element found in some eukaryotes that acts as a protein-binding site and has been found to regulate gene expression in neurons, muscles, and other tissues. Its specific DNA sequence, CANNTG (where N can be any nucleotide), with a palindromic canonical sequence of CACGTG, is recognized and bound by transcription factors to initiate gene transcription. Once the transcription factors bind to the promoters through the E-box, other enzymes can bind to the promoter and facilitate transcription from DNA to mRNA. The E-box was discovered in a collaboration between Susumu Tonegawa's and Walter Gilbert's laboratories in 1985 as a control element in immunoglobulin heavy-chain enhancer. They found that a region of 140 base pairs in the tissue-specific transcriptional enhancer element was sufficient for different levels of transcription enhancement in different tissues and sequences. They suggested that proteins made by specific tissues acted on these enhancers to activate sets of genes during cell differentiation. In 1989, David Baltimore's lab discovered the first two E-box binding proteins, E12 and E47. These immunoglobulin enhancers could bind as heterodimers to proteins through bHLH domains. In 1990, another E-protein, ITF-2A (later renamed E2-2Alt) was discovered that can bind to immunoglobulin light chain enhancers. Two years later, the third E-box binding protein, HEB, was discovered by screening a cDNA library from HeLa cells. A splice-variant of the E2-2 was discovered in 1997 and was found to inhibit the promoter of a muscle-specific gene. Since then, researchers have established that the E-box affects gene transcription in several eukaryotes and found E-box binding factors that identify E-box consensus sequences. In particular, several experiments have shown that the E-box is an integral part of the transcription-translation feedback loop that comprises the circadian clock. E-box binding proteins play a major role in regulating transcriptional activity. These proteins usually contain the basic helix-loop-helix protein structural motif, which allows them to bind as dimers. This motif consists of two amphipathic α-helices, separated by a small sequence of amino acids, that form one or more β-turns. The hydrophobic interactions between these α-helices stabilize dimerization. Besides, each bHLH monomer has a basic region, which helps mediate recognition between the bHLH monomer and the E-box (the basic region interacts with the major groove of the DNA). Depending on the DNA motif ('CAGCTG' versus 'CACGTG') the bHLH protein has a different set of basic residues. The E-box binding is modulated by Zn2+ in mice. The CT-Rich Regions(CTRR) located about 23 nucleotides upstream of the E-box is important in E-box binding, transactivation (increased rate of genetic expression), and transcription of circadian genes BMAL1/NPAS2 and BMAL1/CLOCK complexes. The binding specificity of different E-boxes is found to be essential in their function. E-boxes with different functions have a different number and type of binding factor.