Screening reveals conserved and nonconserved transcriptional regulatory elements including an E3/E4 allele-dependent APOE coding region enhancer

Genomics
Hsuan Pu ChenDesmond J Smith

Abstract

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.

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Citations

Dec 9, 2009·Nucleic Acids Research·Xianjun DongBoris Lenhard
Nov 22, 2013·Genome Biology and Evolution·Isaac Adeyemi Babarinde, Naruya Saitou
Aug 14, 2012·Journal of Neuroinflammation·Eiron CudabackChristopher Dirk Keene
Jul 31, 2013·Human Molecular Genetics·Chang-En YuLynn M Bekris
Mar 29, 2011·Current Opinion in Structural Biology·Stephen C J Parker, Thomas D Tullius
Aug 27, 2010·Biology of Reproduction·Jitu W GeorgeLeslie L Heckert

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