BMC Genomics 2007, 8:99 http://www.biomedcentral.com/1471-2164/8/99 TFrigaunsrceri7ptional activity of the rat proximal HL promoter region in HepG2 and HeLa cells Transcriptional activity of the rat proximal HL promoter region in HepG2 and HeLa cells. HepG2 (hatched bars) and HeLa cells (open bars) were transiently transfected with the indicated promoter-reporter constructs. At 48 h post-trans- fection, transcriptional activity was determined as the ratio of CAT over β-galactosidase expression level. Data are expressed as percentage of the ratio measured in the rHL-39 CAT – transfected cells. Data are means ± SD from 3 independent experi- ments, each performed in triplicate. *,+: P < 0.05 compared to 100% in HepG2 and HeLa cells, respectively. of HNF1α [29]. Since potential HNF4α binding sites were detected in the conserved module A (as well as in the - 295/-265 module), the liver-specific stimulation of HL promoter activity may well be mediated by HNF4α. In fact, HNF4α is bound to the promoter regions of almost half of the actively transcribed genes in human liver [29] and therefore contributes to a large fraction of liver-spe- cific gene expression. Sequence modules that contain both HNF1 and HNF4 binding sites are among the strong- est predictors of liver-specific transcription [10]. Rufibach et al. [25] proposed that HNF1α and HNF4α independ- ently and additively activate HL promoter activity. Which transcription factor(s) mediate inhibition of minimal pro- moter activity in cells of non-hepatic origin, remain(s) unknown at present. Conclusion In summary, we have shown here that a global multispe- cies comparison of non-coding sequences, followed by a search for conserved clusters of TFBS, has predicted the most important sequences involved in basal transcription of the HL gene. This in silico analysis does not identify all regulatory sequences in a particular gene, but enables the intelligent design of experiments towards identification of functional cis-regulatory elements and transactivating fac- tors in gene regulation. This study illustrates the power of Page 10 of 13 (page number not for citation purposes)