Searching for conserved non-coding sequences by comparative genomics is a valuable tool …

• Abstract
• Background
• Results
• Discussion
• Conclusion
• Methods
• List of abbreviations
• References
• Figures
• Tables

Biology Articles » Evolutionary Biology » Comparative Genomics » Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes » References

References

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

1.   Wingender E, Chen X, Fricke E, Geffers R, Hehl R, Liebich I, Krull M, Matys V, Michael H, Ohnhauser R, Pruss M, Schacherer F, Thiele S, Urbach S: The TRANSFAC system on gene expression regulation.Nucleic Acids Res 2001, 29:281-283.       2.   Quandt K, Frech K, Karas H, Wingender E, Werner T: MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data.Nucleic Acids Res 1995, 23:4878-4884.       3.   Fickett JW, Wasserman WW: Discovery and modeling of transcriptional regulatory regions.Curr Opin Biotechnol 2000, 11:19-24.         4.   Zhang Z, Gerstein M: Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements.J Biol 2003, 2:11.       5.   Hardison RC: Conserved noncoding sequences are reliable guides to regulatory elements.Trends Genet 2000, 16:369-372.       6.   Levy S, Hannenhalli S, Workman C: Enrichment of regulatory signals in conserved non-coding genomic sequence.Bioinformatics 2001, 17:871-877.       7.   Cora D, Herrmann C, Dieterich C, Di Cunto F, Provero P, Caselle M: Ab initio identification of putative human transcription factor binding sites by comparative genomics.BMC Bioinformatics 2005, 6:110.       8.   Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, Couronne O, Eisen MB, Visel A, Rubin EM: In vivo enhancer analysis of human conserved non-coding sequences.Nature 2006, 444:499-502.       9.   Wagner A: Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes.Bioinformatics 1999, 15:776-784.       10.   Krivan W, Wasserman WW: A predictive model for regulatory sequences directing liver-specific transcription.Genome Res 2001, 11:1559-1566.       11.   Loots GG, Ovcharenko I, Pachter L, Dubchak I, Rubin EM: rVista for comparative sequence-based discovery of functional transcription factor binding sites.Genome Res 2002, 12:832-839.       12.   Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I: VISTA: computational tools for comparative genomics.Nucleic Acids Res 2004, 32:W273-9.       13.   Doolittle MH, Wong H, Davis RC, Schotz MC: Synthesis of hepatic lipase in liver and extrahepatic tissues.J Lipid Res 1987, 28:1326-1334.       14.   Semenkovich CF, Chen SH, Wims M, Luo CC, Li WH, Chan L: Lipoprotein lipase and hepatic lipase mRNA tissue specific expression, developmental regulation, and evolution.J Lipid Res 1989, 30:423-431.       15.   Perret B, Mabile L, Martinez L, Terce F, Barbaras R, Collet X: Hepatic lipase: structure/function relationship, synthesis, and regulation.J Lipid Res 2002, 43:1163-1169.       16.   Schultz CJ, Blanchette-Mackie EJ, Scow RO: Adrenal and liver in normal and cld/cld mice synthesize and secrete hepatic lipase, but the lipase is inactive in cld/cld mice.J Lipid Res 2000, 41:214-225.       17.   Gonzalez-Navarro H, Nong Z, Freeman L, Bensadoun A, Peterson K, Santamarina-Fojo S: Identification of mouse and human macrophages as a site of synthesis of hepatic lipase.J Lipid Res 2002, 43:671-675.       18.   Jansen H, De Greef WJ: Heparin-releasable lipase activity of rat adrenals, ovaries and testes.Biochem J 1981, 196:739-745.       19.   Hixenbaugh EA, Sullivan TR Jr., Strauss JF 3rd, Laposata EA, Komaromy M, Paavola LG: Hepatic lipase in the rat ovary. Ovaries cannot synthesize hepatic lipase but accumulate it from the circulation.J Biol Chem 1989, 264:4222-4230.       20.   Galan X, Peinado-Onsurbe J, Julve J, Ricart-Jane D, Robert MQ, Llobera M, Ramirez I: Inactive hepatic lipase in rat plasma.J Lipid Res 2003, 44:2250-2256.       21.   Jansen H, Verhoeven AJ, Sijbrands EJ: Hepatic lipase: a pro- or anti-atherogenic protein?J Lipid Res 2002, 43:1352-1362.       22.   Hadzopoulou-Cladaras M, Cardot P: Identification of a cis-acting negative DNA element which modulates human hepatic triglyceride lipase gene expression.Biochemistry 1993, 32:9657-9667.       23.   Oka K, Ishimura-Oka K, Chu MJ, Chan L: Transcription of the human hepatic lipase gene is modulated by multiple negative elements in HepG2 cells.Gene 1996, 180:69-80.       24.   Chang SF, Scharf JG, Will H: Structural and functional analysis of the promoter of the hepatic lipase gene.Eur J Biochem 1997, 247:148-159.       25.   Rufibach LE, Duncan SA, Battle M, Deeb SS: Transcriptional regulation of the human hepatic lipase (LIPC) gene promoter.J Lipid Res 2006, 47:1463-1477.       26.   Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Ouverdin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney E: Ensembl 2007.Nucleic Acids Res 2007, 35:D610-7.       27.   Prabhakar S, Poulin F, Shoukry M, Afzal V, Rubin EM, Couronne O, Pennacchio LA: Close sequence comparisons are sufficient to identify human cis-regulatory elements.Genome Res 2006, 16:855-863.       28.   Shih DQ, Bussen M, Sehayek E, Ananthanarayanan M, Shneider BL, Suchy FJ, Shefer S, Bollileni JS, Gonzalez FJ, Breslow JL, Stoffel M: Hepatocyte nuclear factor-1alpha is an essential regulator of bile acid and plasma cholesterol metabolism.Nat Genet 2001, 27:375-382.       29.   Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, Murray HL, Volkert TL, Schreiber J, Rolfe PA, Gifford DK, Fraenkel E, Bell GI, Young RA: Control of pancreas and liver gene expression by HNF transcription factors.Science 2004, 303:1378-1381.       30.   Ensembl[http://www.ensembl.org]       31.   Vista[http://genome.lbl.gov/vista]       32.   Genomatix Software GmbH[http://www.genomatix.de]       33.   Komaromy MC, Schotz MC: Cloning of rat hepatic lipase cDNA: evidence for a lipase gene family.Proc Natl Acad Sci U S A 1987, 84:1526-1530.       34.   Sambrook J FEF Maniatis T: Molecular Cloning: A Laboratory Manual.Cold Spring Harbor, Cold Spring Harbor Press; 1989.       35.   Sensel MG, Legrand-Lorans A, Wang ME, Bensadoun A: Isolation and characterization of clones for the rat hepatic lipase gene upstream regulatory region.Biochim Biophys Acta 1990, 1048:297-302.       36.   Botma GJ, Verhoeven AJ, Jansen H: Hepatic lipase promoter activity is reduced by the C-480T and G-216A substitutions present in the common LIPC gene variant, and is increased by Upstream Stimulatory Factor.Atherosclerosis 2001, 154:625-632.       37.   Botma GJ, van Deursen D, Vieira D, van Hoek M, Jansen H, Verhoeven AJ: Sterol-regulatory-element binding protein inhibits upstream stimulatory factor-stimulated hepatic lipase gene expression.Atherosclerosis 2005, 179:61-67.       38.   Warren RJ, Ebert DL, Mitchell A, Barter PJ: Rabbit hepatic lipase cDNA sequence: low activity is associated with low messenger RNA levels.J Lipid Res 1991, 32:1333-1339.