Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes

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.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.Understanding transcriptional regulation of gene expression is a major challenge in molecular biology. In eukaryotes, regulation of gene expression is achieved through the complex interaction of transcription factors, which bind to specific DNA sequence motifs. These motifs are predominantly located in the upstream region of genes. Over the last decades, numerous transcription factors have been identified, each with its own specific DNA binding sequence (TFBS). Transcription factors that are potentially involved in the regulation of a particular gene are usually identified by the presence of the specific DNA binding motif in the upstream regulatory region. These binding motifs are compiled in libraries such as the Transfac database [1], and pr