Comparative genomic analysis reveals a distant liver enhancer upstream of the COUP-TFII gene
COUP-TFII is a central nuclear hormone receptor that tightly regulates the expression of numerous target lipid metabolism genes in vertebrates. However, it remains unclear how COUP-TFII itself is transcriptionally controlled since studies with its promoter and upstream region fail to recapitulate the genes liver expression. In an attempt to identify liver enhancers in the vicinity of COUP-TFII, we employed a comparative genomic approach. Initial comparisons between humans and mice of the 3,470kb gene poor region surrounding COUP-TFII revealed 2,023 conserved non-coding elements. To prioritize a subset of these elements for functional studies, we performed further genomic comparisons with the orthologous pufferfish (Fugu rubripes) locus and uncovered two anciently conserved non-coding sequences (CNS) upstream of COUP-TFII (CNS-62kb and CNS-66kb). Testing these two elements using reporter constructs in liver (HepG2) cells revealed that CNS-66kb, but not CNS-62kb, yielded robust in vitro enhancer activity. In addition, an in vivo reporter assay using naked DNA transfer with CNS-66kb linked to luciferase displayed strong reproducible liver expression in adult mice, further supporting its role as a liver enhancer. Together, these studies further support the utility of comparative genomics to uncover gene regulatory sequences based on evolutionary conservation and provide the substrates to better understand the regulation and expression of COUP-TFII.
- Research Organization:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Organization:
- USDOE. Office of Management Budget and Evaluation; National Institutes of Health Grants HL66681 and HL071954A, American Heart Association Postdoctoral Fellowship (US)
- DOE Contract Number:
- AC03-76SF00098
- OSTI ID:
- 838192
- Report Number(s):
- LBNL-56191; R&D Project: GHPG6A; TRN: US200507%%358
- Journal Information:
- Mammalian Genome, Vol. 16, Issue 2; Other Information: Submitted to Mammalian Genome: Volume 16, No.2; Journal Publication Date: 02/2005; PBD: 20 Aug 2004
- Country of Publication:
- United States
- Language:
- English
Similar Records
The expression of Hedgehog genes (Ihh, Dhh) and Hedgehog target genes (Ptc1, Gli1, Coup-TfII) is affected by estrogenic stimuli in the uterus of immature female rats
In Vivo Characterization of a Vertebrate Ultra-conserved Enhancer