BMC Genomics Research article Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes Diederik van Deursen1, Gert-Jan Botma1, Hans Jansen1,2 and Adrie JM Verhoeven*1 BioMed Central Open Access Address: 1Department of Biochemistry, Cardiovascular Research School COEUR, Erasmus MC, PO Box 1738, 3000 DR Rotterdam, The Netherlands and 2Department of Clinical Chemistry, Cardiovascular Research School COEUR, Erasmus MC, PO Box 1738, 3000 DR Rotterdam, The Netherlands Email: Diederik van Deursen - d.vandeursen@erasmusmc.nl; Gert-Jan Botma - GJBotma@prdgb.JNJ.com; Hans Jansen - h.jansen@erasmusmc.nl; Adrie JM Verhoeven* - a.verhoeven@erasmusmc.nl * Corresponding author Published: 11 April 2007 BMC Genomics 2007, 8:99 doi:10.1186/1471-2164-8-99 This article is available from: http://www.biomedcentral.com/1471-2164/8/99 Received: 23 January 2007 Accepted: 11 April 2007 © 2007 van Deursen et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Mammalian hepatic lipase (HL) genes are transcribed almost exclusively in hepatocytes. The basis for this liver-restricted expression is not completely understood. We hypothesized that the responsible cis-acting elements are conserved among mammalian HL genes. To identify these elements, we made a genomic comparison of 30 kb of 5'-flanking region of the rat, mouse, rhesus monkey, and human HL genes. The in silico data were verified by promoter- reporter assays in transfected hepatoma HepG2 and non-hepatoma HeLa cells using serial 5'- deletions of the rat HL (-2287/+9) and human HL (-685/+13) promoter region. Results: Highly conserved elements were present at the proximal promoter region, and at 14 and 22 kb upstream of the transcriptional start site. Both of these upstream elements increased transcriptional activity of the human HL (-685/+13) promoter region 2–3 fold. Within the proximal HL promoter region, conserved clusters of transcription factor binding sites (TFBS) were identified at -240/-200 (module A), -80/-40 (module B), and -25/+5 (module C) by the rVista software. In HepG2 cells, modules B and C, but not module A, were important for basal transcription. Module B contains putative binding sites for hepatocyte nuclear factors HNF1α. In the presence of module B, transcription from the minimal HL promoter was increased 1.5–2 fold in HepG2 cells, but inhibited 2–4 fold in HeLa cells. Conclusion: Our data demonstrate that searching for conserved non-coding sequences by comparative genomics is a valuable tool in identifying candidate enhancer elements. With this approach, we found two putative enhancer elements in the far upstream region of the HL gene. In addition, we obtained evidence that the -80/-40 region of the HL gene is responsible for enhanced HL promoter activity in hepatoma cells, and for silencing HL promoter activity in non-liver cells. Page 1 of 13 (page number not for citation purposes)