Gene transcriptions/Elements/Upstream responses

"Apolipoprotein E (apoE)1 is a major component of various classes of plasma lipoproteins. It is a single-chain polypeptide of 299 amino acids, which plays a prominent role in transport and metabolism of plasma cholesterol and triglycerides, resulting from its ability to interact with lipoprotein receptors (1). The amino acid sequence of the human protein presents two polymorphic sites that generate three isoforms (apoE2, apoE3, and apoE4)."

"URE1 and URE3, upstream response elements 1 and 3 (24, 28)" occur within -163 to -124 and -113 to -80, respectively, and a TATA box within -38 to about -30 nts "of the proximal APOE promoter".

An "unidentified protein was reported to bind to URE3 between -89 and -101 (28)."

"To identify specific sequences in the 5'-flanking region that are significant for human apoE gene expression, portions of the 5‘ ends of this region were progressively deleted by Bal31 nuclease treatment. [...] In both CHO and HepG2 cells, deletion of the 268 nucleotides between -651 and -383, which contains part of an AluI sequence, had little effect on apoE promoter-directed CAT activity. Deletion of the region between nucleotides -383 and -212 resulted in almost a 2-fold reduction in CAT activity. This region contains two types of directly repeated elements: 5‘-TCCAGAT-3’ (-355 to -349, -335 to -329, and -268 to -262) and 5’-CAGGAAAGGA-3’ (-312 to -303 and -296 to -287). In addition, this region contains the hexanucleotide core sequences of an Spl protein binding "GC box" (-279 to -274) (36), but the identities of the neighboring nucleotides indicate that it may be a low affinity binding site (37). Deletion of the sequence between nucleotides -212 and -81 resulted in about a 4-fold reduction in CAT activity in both cell types. The removal of the region between nucleotides -81 and -39 resulted in another 2.5-4-fold reduction in promoter activity. Since this region contains two GC boxes, these results suggest that one or both GC boxes are functional components of the apoE promoter complex. Deletion of the region from nucleotides -39 to -14, which contains a consensus TATA box element, results in an additional 6- to 10-fold decrease in activity. In summary, the results from these deletion studies with the chimeric CAT gene suggest that, in addition to the TATA box in the proximal 383 nucleotides of the 5’-flanking region of human apoE	gene at least three different domains, possibly containing several elements, are involved in the regulation of its transcription."

There "are three elements with enhancer-like properties located within this 1-kb fragment. One element, termed upstream regulatory element 2 (URE2), is located between residues -366 and -246. Another element, termed upstream regulatory element 1 (UREl), was found in a fragment located between residues -246 and -81; UREl is located within a 69-bp segment between residues -193 and -124 of this fragment. The third element, termed intron regulatory element1 (IREl), was found within the first intron and is located in a 219-bp segment between residues +44 and +262. These three elements had promoter-enhancing activity in both orientations."

URE1 is apparently 5'-ACCTCTATGCCCCACCTCCTTC-3' or contained in it between -193 to -124. URE2 is apparently contained in -366 to -246.

URE1 may be 5‘-AGGAG(G/C)(T/G)GGGG(C/T)-3'.

"The sequence of the URE1 protein binding region [...] contains inverted repeated sequences (-164 to -159, -152	to -147, 5‘-ACCTCTATGCCCCACCTCCTTC-3’)."