Screening reveals conserved and nonconserved transcriptional regulatory elements including an E3/E4 allele-dependent APOE coding region enhancer.
We performed an unbiased experimental search for enhancers and silencers in a 153-kb region containing the human apolipoprotein (APO) E/C1/C4/C2 gene cluster using shotgun cloning into a luciferase vector. A continuum of transcriptional effect sizes was observed, possibly explaining the limited success of bioinformatics in identifying regulatory regions. We identified nine statistically significant enhancers and five silencers functional in either liver or astrocyte cells, including two previously known enhancers. Only two of the fourteen elements contained conserved noncoding sequences. Within the coding sequence of the APOE gene we identified an enhancer for the E4 allele associated with Alzheimer's disease, but not E3. The single nucleotide polymorphism (SNP) causing the E4/E3 amino acid substitution was responsible for these variations, potentially explaining the higher expression levels of E4. Our results suggest a wider variety of mammalian transcriptional regulatory sequences than is currently recognized and that these may include coding region SNPs.
Chen
Hsuan Pu
HP
Department of Biomedical Engineering, University of California, Los Angeles, CA 90095, USA.
Lin
Andy
A
Bloom
Joshua S
JS
Khan
Arshad H
AH
Park
Christopher C
CC
Smith
Desmond J
DJ
D000483:Alleles; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D053318:Apolipoprotein E3 / Q000737:chemistry / Q000235:genetics; D053327:Apolipoprotein E4 / Q000737:chemistry / Q000235:genetics*; D001057:Apolipoproteins E / Q000235:genetics*; D001253:Astrocytes; D001483:Base Sequence; D002460:Cell Line; D003001:Cloning, Molecular / Q000379:methods; D017124:Conserved Sequence; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D018628:Gene Dosage; D005822:Genetic Vectors; D006801:Humans; D008099:Liver / Q000166:cytology; D008156:Luciferases / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family; D020641:Polymorphism, Single Nucleotide; D050436:Regulatory Elements, Transcriptional
D053318:Apolipoprotein E3; D053327:Apolipoprotein E4; D001057:Apolipoproteins E; D008156:Luciferases