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Trends Biochem Sci. 2002, 27: 67-74.\nBarrett AJ, Rawlings ND, Woessner JF: Handbook of proteolytic enzymes. 1998, San Diego: Academic press,\nKorkmaz B, Moreau T, Gauthier F: Neutrophil elastase, proteinase 3 and cathepsin G: Physicochemical properties, activity and physiopathological functions. Biochimie. 2008, 90: 227-242.\nHedstrom L: Serine protease mechanism and specificity. Chem Rev. 2002, 102: 4501-4524.\nVolanakis JE, Narayana SV: Complement factor D, a novel serine protease. Protein Sci. 1996, 5: 553-564.\nAdham IM, Klemm U, Maier WM, Hoyer-Fender S, Tsaousidou S, Engel W: Molecular cloning of preproacrosin and analysis of its expression pattern in spermatogenesis. Eur J Biochem. 1989, 182: 563-568.\nKrem MM, Rose T, Di Cera E: Sequence Determinants of Function and Evolution in Serine Proteases. Trends in Cardiovascular Medicine. 2000, 10: 171-176.\nHaley SA, Wessel GM: Regulated proteolysis by cortical granule serine protease 1 at fertilization. Mol Biol Cell. 2004, 15: 2084-2092.\nHaley SA, Wessel GM: Proteolytic cleavage of the cell surface protein p160 is required for detachment of the fertilization envelope in the sea urchin. Dev Biol. 2004, 272: 191-202.\nYe Y, Fortini ME: Proteolysis and developmental signal transduction. Semin Cell Dev Biol. 2000, 11: 211-221.\nLeMosy EK, Tan YQ, Hashimoto C: Activation of a protease cascade involved in patterning the Drosophila embryo. Proc Natl Acad Sci USA. 2001, 98: 5055-5060.\nTerada T, Okada Y, Nakanuma Y: Expression of matrix proteinases during human intrahepatic bile duct development. A possible role in biliary cell migration. Am J Pathol. 1995, 147: 1207-1213.\nDrapkin PT, Monard D, Silverman AJ: The role of serine proteases and serine protease inhibitors in the migration of gonadotropin-releasing hormone neurons. BMC Dev Biol. 2002, 2: 1-\nGiorgi F, Bradley JT, Nordin JH: Differential vitellin polypeptide processing in insect embryos. Micron. 1999, 30: 579-596.\nAbreu LA, Valle D, Manso PP, Facanha AR, Pelajo-Machado M, Masuda H, Masuda A, Vaz I, Lenzi H, Oliveira PL, Logullo C: Proteolytic activity of Boophilus microplus Yolk pro-Cathepsin D (BYC) is coincident with cortical acidification during embryogenesis. Insect Biochem Mol Biol. 2004, 34: 443-449.\nIndrasith LS, Sasaki T, Yamashita O: A unique protease responsible for selective degradation of a yolk protein in Bombyx mori. Purification, characterization, and cleavage profile. J Biol Chem. 1988, 263: 1045-1051.\nMedina M, Vallejo CG: A Serine Proteinase in Drosophila Embryos – Yolk Localization and Developmental Activation. Insect Biochemistry. 1989, 19: 687-691.\nIkeda M, Yaginuma T, Kobayashi M, Yamashita O: Cdna Cloning, Sequencing and Temporal Expression of the Protease Responsible for Vitellin Degradation in the Silkworm, Bombyx-Mori. Comparative Biochemistry and Physiology B-Biochemistry & Molecular Biology. 1991, 99: 405-411.\nIkeda M, Sasaki T, Yamashita O: Purification and Characterization of Proteases Responsible for Vitellin Degradation of the Silkworm, Bombyx-Mori. Insect Biochemistry. 1990, 20: 725-\nEstrela A, Seixas A, Termignoni C: A cysteine endopeptidase from tick (Rhipicephalus (Boophilus) microplus) larvae with vitellin digestion activity. Comparative Biochemistry and Physiology B-Biochemistry & Molecular Biology. 2007, 148: 410-416.\nMedina M, Leon P, Vallejo CG: Drosophila cathepsin B-like proteinase: a suggested role in yolk degradation. Arch Biochem Biophys. 1988, 263: 355-363.\nFagotto F: Regulation of yolk degradation, or how to make sleepy lysosomes. J Cell Sci. 1995, 108 (Pt 12): 3645-3647.\nLeMosy EK, Kemler D, Hashimoto C: Role of Nudel protease activation in triggering dorsoventral polarization of the Drosophila embryo. Development. 1998, 125: 4045-4053.\nBonnier P, Baert JL: Identification of Cathepsin L-Like Proteinase and Aminopeptidase in Yolk Granules of the Sand Worm, Nereis-Diversicolor. Comparative Biochemistry and Physiology B-Biochemistry & Molecular Biology. 1992, 103: 425-430.\nCho WL, Deitsch KW, Raikhel AS: An extraovarian protein accumulated in mosquito oocytes is a carboxypeptidase activated in embryos. Proc Natl Acad Sci USA. 1991, 88: 10821-10824.\nRibolla PEM, Debianchi AG: Processing of Procathepsin from Musca-Domestica Eggs. Insect Biochem Mol Biol. 1995, 25: 1011-1017.\nTadros W, Goldman AL, Babak T, Menzies F, Vardy L, Orr-Weaver T, Hughes TR, Westwood JT, Smibert CA, Lipshitz HD: SMAUG is a major regulator of maternal mRNA destabilization in Drosophila and its translation is activated by the PAN GU kinase. Dev Cell. 2007, 12: 143-155.\nDe Renzis S, Elemento O, Tavazoie S, Wieschaus E: Unmasking activation of the zygotic genome using chromosomal deletions in the drosophila embryo (vol 5, art. no. e117, 2007). Plos Biology. 2007, 5: 1631-1631.\nPike AW, Wadsworth SL: Sealice on Salmonids: Their Biology and Control. Adv Parasitol. 1999, 44: 233-337.\nKvamme BO, Frost P, Nilsen F: The cloning and characterisation of full-length trypsins from the salmon louse Lepeophtheirus salmonis. Mol Biochem Parasitol. 2004, 136: 303-307.\nKvamme BO, Skern R, Frost P, Nilsen F: Molecular characterisation of five trypsin-like peptidase transcripts from the salmon louse (Lepeophtheirus salmonis) intestine. Int J Parasitol. 2004, 34: 823-832.\nKvamme BO, Kongshaug H, Nilsen F: Organisation of trypsin genes in the salmon louse (Lepeophtheirus salmonis, Crustacea, copepoda) genome. Gene. 2005, 352: 63-74.\nSkern-Mauritzen R, Frost P, Hamre LA, Kongshaug H, Nilsen F: Molecular characterization and classification of a clip domain containing peptidase from the ectoparasite Lepeophtheirus salmonis (Copepoda, Crustacea). Comparative Biochemistry and Physiology B-Biochemistry & Molecular Biology. 2007, 146: 289-298.\nEmanuelsson O, Brunak S, von Heijne G, Nielsen H: Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc. 2007, 2: 953-971.\nHartley BS: Amino-Acid Sequence of Bovine Chymotrypsinogen-A. Nature. 1964, 201: 1284-1287.\nLesk AM, Fordham WD: Conservation and variability in the structures of serine proteinases of the chymotrypsin family. J Mol Biol. 1996, 258: 501-537.\nJohnson SC, Ewart KV, Osborne JA, Delage D, Ross NW, Murray HM: Molecular cloning of trypsin cDNAs and trypsin gene expression in the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae). Parasitol Res. 2002, 88: 789-796.\nEichner C, Frost P, Dysvik B, Jonassen I, Kristiansen B, Nilsen F: Salmon louse (Lepeophtheirus salmonis) transcriptomes during post molting maturation and egg production, revealed using EST-sequencing and microarray analysis. BMC Genomics. 2008, 9: 126-\nMuller HM, Crampton JM, della Torre A, Sinden R, Crisanti A: Members of a trypsin gene family in Anopheles gambiae are induced in the gut by blood meal. EMBO J. 1993, 12: 2891-2900.\nOhmura K, Kohno N, Kobayashi Y, Yamagata K, Sato S, Kashiwabara S, Baba T: A homologue of pancreatic trypsin is localized in the acrosome of mammalian sperm and is released during acrosome reaction. J Biol Chem. 1999, 274: 29426-29432.\nBrunel C, Ehresmann C: Secondary structure of the 3' UTR of bicoid mRNA. Biochimie. 2004, 86: 91-104.\nLewis RA, Kress TL, Cote CA, Gautreau D, Rokop ME, Mowry KL: Conserved and clustered RNA recognition sequences are a critical feature of signals directing RNA localization in Xenopus oocytes. Mech Dev. 2004, 121: 101-109.\nLie YS, Macdonald PM: Apontic binds the translational repressor Bruno and is implicated in regulation of oskar mRNA translation. Development. 1999, 126: 1129-1138.\nBullock SL, Zicha D, Ish-Horowicz D: The Drosophila hairy RNA localization signal modulates the kinetics of cytoplasmic mRNA transport. EMBO J. 2003, 22: 2484-2494.\nBashirullah A, Cooperstock RL, Lipshitz HD: Spatial and temporal control of RNA stability. Proc Natl Acad Sci USA. 2001, 98: 7025-7028.\nWilson CB: North American Parasitic Copepods belonging to the Family Caligidae. Part I – The Caliginae. Proceedings of the US National Museum. 1905, 28: 479-672.\nMcClendon JF: On the development of parasitic copepods – Part II. Biol Bull. 1907, 12: 53-88.\nMcClendon JF: On the development of parasitic copepods – Part I. Biol Bull. 1906, 12: 37-52.\nDe Renzis S, Elemento O, Tavazoie S, Wieschaus EF: Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo. PLoS Biol. 2007, 5: e117-\nEzquieta B, Vallejo CG: The Trypsin-Like Proteinase of Artemia – Yolk Localization and Developmental Activation. Comparative Biochemistry and Physiology B-Biochemistry & Molecular Biology. 1985, 82: 731-736.\nMedina M, Vallejo CG: The Maternal Origin of Acid-Hydrolases in Drosophila and Their Relation with Yolk Degradation. Development Growth & Differentiation. 1989, 31: 241-247.\nRibolla PEM, Bijovsky AT, de Bianchi AG: Procathepsin and acid phosphatase are stored in Musca domestica yolk spheres. Journal of Insect Physiology. 2001, 47: 225-232.\nFausto AM, Gambellini G, Mazzini M, Cecchettini A, Masetti M, Giorgi F: Yolk granules are differentially acidified during embryo development in the stick insect Carausius morosus. Cell Tissue Res. 2001, 305: 433-443.\nFrost P, Nilsen F: Validation of Reference Genes for Transcription Profiling in the Salmon Louse, Lepeophtheirus Salmonis, by Quantitative Real-Time Pcr. Veterinary Parasitology. 2003, 118: 169-174.\nEmanuelsson O, Nielsen H, Brunak S, von Heijne G: Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol. 2000, 300: 1005-1016.\nBendtsen JD, Nielsen H, von Heijne G, Brunak S: Improved prediction of signal peptides: SignalP 3.0. J Mol Biol. 2004, 340: 783-795.\nKrogh A, Larsson B, von Heijne G, Sonnhammer EL: Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001, 305: 567-580.\nGromiha MM, Ahmad S, Suwa M: Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins. J Comput Chem. 2004, 25: 762-767.\nEisenhaber B, Bork P, Eisenhaber F: Prediction of potential GPI-modification sites in proprotein sequences. J Mol Biol. 1999, 292: 741-758.\nFelsenstein J: PHYLIP (Phylogeny Inference Package) version 3.6. 2004,\nStrimmer K, vonHaeseler A: Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies. Mol Biol Evol. 1996, 13: 964-969.\nLivak KJ, Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001, 25: 402-408.\nPeirson SN, Butler JN, Foster RG: Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis. Nucleic Acids Res. 2003, 31: 1-7.\nSkern R, Frost P, Nilsen F: Relative transcript quantification by Quantitative PCR: Roughly right or precisely wrong?. Bmc Molecular Biology. 2005, 6: 10-DOI 10.1186\u002F1471-2199-6-10,\nSommerset I, Skern R, Biering E, Bleie H, Fiksdal IU, Grove S, Nerland AH: Protection against Atlantic halibut nodavirus in turbot is induced by recombinant capsid protein vaccination but not following DNA vaccination. Fish Shellfish Immunol. 2005, 18: 13-29.",{"EN":138},"Trypsin-like serine proteases are involved in a large number of processes including digestive degradation, regulation of developmental processes, yolk degradation and yolk degradome activation. Trypsin like peptidases considered to be involved in digestion have been characterized in Lepeophtheirus salmonis. During these studies a trypsin-like peptidase which differed in a number of traits were identified. An intronless trypsin-like serine peptidase (LsTryp10) from L., salmonis was identified and characterized. LsTryp10 mRNA is evenly distributed in the ovaries and oocytes, but is located along the ova periphery. LsTryp10 protein is deposited in the oocytes and all embryonic cells. LsTryp10 mRNA translation and concurrent degradation after fertilization was found in the embryos demonstrating that LsTryp10 protein is produced both by the embryo and maternally. The results furthermore indicate that LsTryp10 protein of maternal origin has a distribution pattern different to that of embryonic origin. Based on present data and previous studies of peptidases in oocytes and embryos, we hypothesize that maternally deposited LsTryp10 protein is involved in regulation of the yolk degradome. The function of LsTryp10 produced by the embryonic cells remains unknown. 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AH, Berta P, Palmer MS, Hawkins JR, Griffiths BL, Smith MJ, Foster JW, Frischauf AM, Lovell-Badge R, Goodfellow PN: A gene from the human sex determining region encodes a protein with homology to a conserved DNA-binding motif. Nature. 1990, 364: 240-244. 10.1038\u002F346240a0. 10.1038\u002F346240a0\nGubbay J, Collignon J, Koopman P, Capel B, Economou A, Münsterberg A, Vivian N, Goodfellow P, Lovell-Badge R: A gene mapping to the sex-determining region of the mouse Y chromosome is a member of a novel family of embryonically expressed genes. Nature. 1990, 346: 245-250. 10.1038\u002F346245a0\nKoopman P, Gubbay J, Vivian N, Goodfellow P, Lovell-Badge R: Male development of chromosomally female mice transgenic for Sry. Nature. 1991, 351: 117-121. 10.1038\u002F351117a0\nWilson MJ, Dearden PK: Evolution of the insect Sox genes. BMC Evol Biol. 2008, 8: 120- 10.1186\u002F1471-2148-8-120\nPevny LH, Lovell-Badge R: Sox genes find their feet. Curr Opin Genet Dev. 1997, 7: 338-344. 10.1016\u002FS0959-437X(97)80147-5\nSchepers GE, Teasdale RD, Koopman P: Twenty pairs of Sox: extent, homology, and nomenclature of the mouse and human Sox transcription factor gene families. Dev Cell. 2002, 3: 167-170. 10.1016\u002FS1534-5807(02)00223-X\nLefebvre V, Dumitriu B, Penzo-Méndez A, Han Y, Pallavi B: Control of cell fate and differentiation by Sry-related highmobility-group box (Sox) transcription factors. Int J Biochem Cell Biol. 2007, 39: 2195-2214. 10.1016\u002Fj.biocel.2007.05.019\nBowles J, Schepers G, Koopman P: Phylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators. Dev Biol. 2000, 227: 239-255. 10.1006\u002Fdbio.2000.9883\nHacker A, Capel B, Goodfellow P, Lovell-Badge R: Expression of Sry, the mouse sex determining gene. Development. 1995, 121: 1603-1614.\nCollignon J, Sockanathan S, Hacker A, Cohen-Tannoudji M, Norris D, Rastan S, Stevanovic M, Goodfellow PN, Lovell-Badge R: A comparison of the properties of Sox-3 with Sry and two related genes, Sox-1 and Sox-2. Development. 1996, 122: 509-520.\nJay P, Goze C, Marsollier C, Taviaux S, Hardelin JP, Koopman P, Berta P: The human SOX11 gene: cloning, chromosomal assignment and tissue expression. Genomics. 1995, 29: 541-545. 10.1006\u002Fgeno.1995.9970\nJay P, Sahly I, Goze C, Taviaux S, Poulat F, Couly G, Abitbol M, Berta P: SOX22 is a new member of the SOX gene family, mainly expressed in human nervous tissue. Hum Mol Genet. 1997, 6: 1069-1077. 10.1093\u002Fhmg\u002F6.7.1069\nWright E, Hargrave MR, Christiansen J, Cooper L, Kun J, Evans T, Gangadharan U, Greenfield A, Koopman P: The Sry-related gene Sox9 is expressed during chondrogenesis in mouse embryos. Nat Genet. 1995, 9: 15-20. 10.1038\u002Fng0195-15\nCohen-Barak O, Hagiwara N, Arlt MF, Horton JP, Brilliant MH: Cloning, characterization and chromosome mapping of the human SOX6 gene. Gene. 2001, 265: 157-164. 10.1016\u002FS0378-1119(01)00346-8\nKanai Y, Kanai-Azuma M, Noce T, Saido TC, Hayashi Y, Yazaki K: Identification of two Sox17 messenger RNA isoforms, with and without the high mobility group box region, and their differential expression in mouse spermatogenesis. J Cell Biol. 1996, 133: 667-681. 10.1083\u002Fjcb.133.3.667\nOsaki E, Inazawa J, Copeland NG, Gilbert DJ, Jenkins NA, Ohsugi M, Tezuka T, Yoshida M, Semba K: Identification of a novel Sry-related gene and its germ cell-specific expression. Nucleic Acids Res. 1999, 27: 2503-2510. 10.1093\u002Fnar\u002F27.12.2503\nStevanovic M, Lovell-Badge R, Collignon J, Goodfellow PN: SOX3 is an X-linked gene related to SRY. Hum Mol Genet. 1993, 2: 2013-2018. 10.1093\u002Fhmg\u002F2.12.2013\nBallow D, Meistrich ML, Matzuk M, Rajkovic A: Sohlh1 is essential for spermatogonial differentiation. Dev Biol. 2006, 294: 161-167. 10.1016\u002Fj.ydbio.2006.02.027\nKoopman P, Schepers G, Brenner S, Venkatesh B: Origin and diversity of the SOX transcription factor gene family: genome-wide analysis in Fugu rubripes. Gene. 2004, 17: 177-186. 10.1016\u002Fj.gene.2003.12.008. 10.1016\u002Fj.gene.2003.12.008\nDe Martino SP, Errington F, Ashworth A, Jowett T, Austin CA: Sox30: a novel zebrafish sox gene expressed in a restricted manner at the midbrain-hindbrain boundary during neurogenesis. Dev Genes Evol. 1999, 209: 357-362. 10.1007\u002Fs004270050264\nWang DS, Jiao B, Hu C, Huang X, Liu Z, Cheng CH: Discovery of a gonad-specific IGF subtype in teleost. Biochem Biophys Res Commun. 2008, 367: 336-341. 10.1016\u002Fj.bbrc.2007.12.136\nKobayashi T, Kajiura-Kobayashi H, Nagahama Y: Induction of XY sex reversal by estrogen involves altered gene expression in a teleost, tilapia. Cytogenet Genome Res. 2003, 101: 289-294. 10.1159\u002F000074351\nZhang WL, Zhou LY, Senthilkumaran B, Sudhakumari CC, Kobayashi T, Nagahama Y, Wang DS: Molecular cloning of two isoforms of 11β-hydroxylase and their expressionsin the Nile tilapia, Oreochromis niloticus. Gen Comp Endocrinol. 2010, 165: 34-41. 10.1016\u002Fj.ygcen.2009.05.018\nZhou L, Wang D, Kobayashi T, Yano A, Paul-Prasanth B, Suzuki A, Sakai F, Nagahama Y: A novel type of P450c17, lacking the lyase activity is responsible for C21-steroid biosynthesis in the fish ovary and head kidney. Endocrinology. 2007, 148: 4282-4291. 10.1210\u002Fen.2007-0487\nJiao BW, Huang XG, Chan CB, Zhang L, Wang DS, Cheng CHK: The co-existence of two growth hormone receptors in teleost fish and their differential signal transduction, tissue distribution and hormonal regulation of expression in seabream. J Mol Endocrinol. 2006, 36: 23-40. 10.1677\u002Fjme.1.01945\nWang D, Kobayashi T, Zhou L, Nagahama Y: Molecular cloning and gene expression of Foxl2 in the Nile tilapia, Oreochromis niloticus. Biochem Biophys Res Commun. 2004, 320: 83-89. 10.1016\u002Fj.bbrc.2004.05.133\nPhochanukul N, Russell S: No backbone but lots of Sox: Invertebrate Sox genes. Int J Biochem Cell Biol. 2010, 42: 453-464. 10.1016\u002Fj.biocel.2009.06.013\nNagai K: Molecular evolution of Sry and Sox gene. Gene. 2001, 270: 161-169. 10.1016\u002FS0378-1119(01)00479-6\nHett AK, Ludwig A: SRY-related (Sox) genes in the genome of European Atlantic sturgeon (Acipenser sturio). Genome. 2005, 48: 181-186.\nJohnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, Armour CD, Santos R, Schadt EE, Stoughton R, Shoemaker DD: Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science. 2003, 302: 2141-2144. 10.1126\u002Fscience.1090100\nSmith CW, Valcárcel J: Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem Sci. 2000, 25: 381-388. 10.1016\u002FS0968-0004(00)01604-2\nTakase M, Noguchi S, Nakamura M: Two Sox9 messenger RNA isoforms: isolation of cDNAs and their expression during gonadal development in the frog, Rana rugosa. FEBS Lett. 2000, 466: 249-254. 10.1016\u002FS0014-5793(00)01078-4\nSakai N, Terami H, Suzuki S, Haga M, Nomoto K, Tsuchida N, Morohashi K, Saito N, Asada M, Hashimoto M, Harada D, Asahara H, Ishikawa T, Shimada F, Sakurada K: Identification of NR5A1 (SF-1\u002FAD4BP) gene expression modulators by large-scale gain and loss of function studies. J Endocrinol. 2008, 198: 489-497. 10.1677\u002FJOE-08-0027\nWang DS, Kobayashi T, Zhou LY, Paul-Prasanth B, Ijiri S, Sakai F, Okubo K, Morohashi K, Nagahama Y: Foxl2 up-regulates aromatase gene transcription in a female-specific manner by binding to the promoter as well as interacting with ad4 binding protein\u002Fsteroidogenic factor 1. Molecular Endocrinology. 2007, 21: 712-725. 10.1210\u002Fme.2006-0248\nWang DS, Zhou LY, Kobayashi T, Matsuda M, Shibata Y, Sakai F, Nagahama Y: Dmrt1 repression of aromatase transcription, a possible mechanism favoring the male pathway in tilapia. Endocrinology. 2010, 151: 1331-1340. 10.1210\u002Fen.2009-0999",{"EN":291},"Members of the Sox gene family isolated from both vertebrates and invertebrates have been proved to participate in a wide variety of developmental processes, including sex determination and differentiation. Among these members, Sox30 had been considered to exist only in mammals since its discovery, and its exact function remains unclear. Sox30 cDNA was cloned from the Nile tilapia by RT-PCR and RACE. Screening of available genome and EST databases and phylogenetic analysis showed that Sox30 also exists in non-mammalian vertebrates and invertebrates, which was further supported by synteny analyses. Tissue expression in human, mouse and tilapia suggested that Sox30 was probably a gonad-specific gene, which was also supported by the fact that Sox30 EST sequences were obtained from gonads of the animal species. In addition, four alternatively spliced isoforms were isolated from tilapia gonad. Their temporal and spatial expression patterns during normal and sex reversed gonadal development were investigated by RT-PCR and in situ hybridization. Our data suggest that expressions of Sox30 isoforms are related to stage and phenotypic-sex, observed in the germ cells of male gonad and in somatic cells of the female gonad. Sox30 is not a gene only existed in mammals, but exists widely throughout the animal kingdom as supported by our bioinformatic, phylogenetic and syntenic analyses. It is very likely that Sox30 is expressed exclusively in gonads. Expression analyses revealed that Sox30 may be involved in female and male gonadal development at different stages by alternative splicing.",{"EN":293},"Characterization, phylogeny, alternative splicing and expression of Sox30 gene",{"VOID":295},"10.1186\u002F1471-2199-11-98","VERIFIED","Auto 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Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China",{"title":315},{"VI":316},"Baofeng Huang",{"id":318,"sortIndex":148,"researcher":18,"roles":319,"affiliations":320,"properties":326},"09e2d3ba-5b3e-4833-ad3e-8dbac239b053",[150],[321],{"id":18,"sortIndex":19,"affiliation":322,"properties":18},{"id":306,"createTime":307,"updateTime":308,"relativeEntities":323,"slug":310,"properties":324,"entityType":39,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"syncStatus":17,"languages":18,"translateLanguages":18,"viewCount":19},[],{"title":325},{"VI":313},{"title":327},{"VI":328},"Deshou 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Wang",{"id":354,"sortIndex":19,"researcher":18,"roles":355,"affiliations":356,"properties":362},"29d6216d-86a2-47cd-a1a7-45d72c7e0f21",[150],[357],{"id":18,"sortIndex":19,"affiliation":358,"properties":18},{"id":306,"createTime":307,"updateTime":308,"relativeEntities":359,"slug":310,"properties":360,"entityType":39,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"syncStatus":17,"languages":18,"translateLanguages":18,"viewCount":19},[],{"title":361},{"VI":313},{"title":363},{"VI":364},"Fei Han",{"id":366,"sortIndex":74,"researcher":18,"roles":367,"affiliations":368,"properties":374},"0fe0cea5-292e-4e85-980b-8ecd0cd95954",[150],[369],{"id":18,"sortIndex":19,"affiliation":370,"properties":18},{"id":306,"createTime":307,"updateTime":308,"relativeEntities":371,"slug":310,"properties":372,"entityType":39,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"syncStatus":17,"languages":18,"translateLanguages":18,"viewCount":19},[],{"title":373},{"VI":313},{"title":375},{"VI":376},"Fengrui Wu",{"url":298,"publisher":378,"properties":398},{"id":6,"createTime":7,"updateTime":8,"relativeEntities":379,"slug":10,"properties":380,"entityType":16,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"syncStatus":17,"languages":18,"translateLanguages":18,"viewCount":19,"subjectFields":383,"manageAffiliations":384,"indexDatabases":385,"url":18,"thumbnailPath":18,"statistic":393,"gsStatistic":18,"type":18,"analyzePriority":18},[],{"eissn":381,"title":382},{"VOID":13},{"EN":15},[],[],[386],{"id":44,"indexDatabase":387,"url":57,"indexYears":58,"academicFieldIds":392,"indexDatabaseRanking":61},{"id":46,"createTime":47,"updateTime":48,"relativeEntities":388,"label":389,"description":390,"key":54,"publicationTags":391,"standard":18},[],{"EN":51,"VI":51},{"EN":51,"VI":53},[56],[60],{"impactFactor":19,"impactFactorByYear":394,"i10Index":73,"i10IndexLast5Year":74,"totalPublication":75,"totalPublicationByYear":395,"totalCitation":92,"totalCitationByYear":396,"totalCitationPerPublication":108,"totalCitationPerPublicationByYear":397,"hindexLast5Year":125,"hindex":125},{"2012":64,"2013":65,"2014":66,"2015":67,"2016":67,"2017":68,"2018":69,"2019":70,"2020":71,"2021":72},{"2000":77,"2001":78,"2002":79,"2003":78,"2004":80,"2005":81,"2006":82,"2007":83,"2008":84,"2009":84,"2010":85,"2011":86,"2012":87,"2013":88,"2014":89,"2015":81,"2016":90,"2017":91,"2018":79,"2019":89},{"2005":94,"2006":95,"2007":96,"2008":97,"2009":98,"2010":99,"2011":100,"2012":101,"2013":102,"2014":103,"2015":104,"2016":78,"2017":105,"2018":106,"2019":107},{"2005":110,"2006":111,"2007":112,"2008":113,"2009":114,"2010":115,"2011":116,"2012":117,"2013":118,"2014":119,"2015":120,"2016":121,"2017":122,"2018":123,"2019":124},{"volume":399,"pages":401},{"VOID":400},"11",{"VOID":277},"2010-12-11",2010,{"id":405,"createTime":406,"updateTime":407,"relativeEntities":408,"slug":409,"properties":410,"entityType":143,"verifyStatus":296,"verifyTime":407,"verifyNote":297,"syncStatus":17,"languages":18,"translateLanguages":18,"viewCount":19,"primaryUrl":419,"fullTextUrl":18,"authors":420,"publicationType":251,"publisherRelationship":463,"citationCount":18,"citationInfo":18,"publishDate":489,"publishYear":490,"citationAnalyzeStatus":17,"lastCitationAnalyze":18,"indexDatabases":18,"openAccess":18,"references":18,"isForceReanalyzing":280},"ff00be15-477b-4553-8547-0d584236b394","2023-12-06T17:41:59.794+00:00","2024-12-08T23:57:24.274+00:00",[],"Expression-of-yeast-lipid-phosphatase-Sac1p-is-regulated-by-phosphatidylinositol-4-phosphate",{"references":411,"abstract":413,"title":415,"doi":417},{"VOID":412},"Di Paolo G, De Camilli P: Phosphoinositides in cell regulation and membrane dynamics. Nature 2006, 443: 651-7. 10.1038\u002Fnature05185.\nBehnia R, Munro S: Organelle identity and the signposts for membrane traffic. Nature 2005, 438: 597-604. 10.1038\u002Fnature04397.\nDe Matteis MA, Di Campli A, Godi A: The role of the phosphoinositides at the Golgi complex. Biochim Biophys Acta 2005, 1744: 396-405. 10.1016\u002Fj.bbamcr.2005.04.013.\nPendaries C, Tronchere H, Plantavid M, Payrastre B: Phosphoinositide signaling disorders in human diseases. FEBS Lett 2003, 546: 25-31. 10.1016\u002FS0014-5793(03)00437-X.\nCarman GM, Henry SA: Phospholipid biosynthesis in the yeast Saccharomyces cerevisiae and interrelationship with other metabolic processes. Prog Lipid Res 1999, 38: 361-99. 10.1016\u002FS0163-7827(99)00010-7.\nJesch SA, Zhao X, Wells MT, Henry SA: Genome-wide analysis reveals inositol, not choline, as the major effector of Ino2p-Ino4p and unfolded protein response target gene expression in yeast. J Biol Chem 2005, 280: 9106-18. 10.1074\u002Fjbc.M411770200.\nLoewen CJ, Gaspar ML, Jesch SA, Delon C, Ktistakis NT, Henry SA, Levine TP: Phospholipid metabolism regulated by a transcription factor sensing phosphatidic acid. Science 2004, 304: 1644-7. 10.1126\u002Fscience.1096083.\nTahirovic S, Schorr M, Mayinger P: Regulation of intracellular phosphatidylinositol-4-phosphate by the Sac1 lipid phosphatase. Traffic 2005, 6: 116-30. 10.1111\u002Fj.1600-0854.2004.00255.x.\nRoy A, Levine TP: Multiple pools of phosphatidylinositol 4-phosphate detected using the pleckstrin homology domain of Osh2p. J Biol Chem 2004, 279: 44683-9. 10.1074\u002Fjbc.M401583200.\nFoti M, Audhya A, Emr SD: Sac1 lipid phosphatase and stt4 phosphatidylinositol 4-kinase regulate a pool of phosphatidylinositol 4-phosphate that functions in the control of the actin cytoskeleton and vacuole morphology. Mol Biol Cell 2001, 12: 2396-411.\nFaulhammer F, Konrad G, Brankatschk B, Tahirovic S, Knodler A, Mayinger P: Cell growth-dependent coordination of lipid signaling and glycosylation is mediated by interactions between Sac1p and Dpm1p. J Cell Biol 2005, 168: 185-91. 10.1083\u002Fjcb.200407118.\nZhu J, Zhang MQ: SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 1999, 15: 607-11. 10.1093\u002Fbioinformatics\u002F15.7.607.\nHughes WE, Pocklington MJ, Orr E, Paddon CJ: Mutations in the Saccharomyces cerevisiae gene SAC1 cause multiple drug sensitivity. Yeast 1999, 15: 1111-24. 10.1002\u002F(SICI)1097-0061(199908)15:11\u003C1111::AID-YEA440>3.0.CO;2-H.\nCleves AE, Novick PJ, Bankaitis VA: Mutations in the SAC1 gene suppress defects in yeast Golgi and yeast actin function. J Cell Biol 1989, 109: 2939-2950. 10.1083\u002Fjcb.109.6.2939.\nKochendorfer KU, Then AR, Kearns BG, Bankaitis VA, Mayinger P: Sac1p plays a crucial role in microsomal ATP transport, which is distinct from its function in Golgi phospholipid metabolism. Embo J 1999, 18: 1506-15. 10.1093\u002Femboj\u002F18.6.1506.\nTahirovic S, Schorr M, Then A, Berger J, Schwarz H, Mayinger P: Role for lipid signaling and the cell integrity MAP kinase cascade in yeast septum biogenesis. Curr Genet 2003, 43: 71-8.\nWhitters EA, Cleves AE, McGee TP, Skinner HB, Bankaitis VA: SAC1p is an integral membrane protein that influences the cellular requirement for phospholipid transfer protein function and inositol in yeast. J Cell Biol 1993, 122: 79-94. 10.1083\u002Fjcb.122.1.79.\nBachhawat N, Ouyang Q, Henry SA: Functional characterization of an inositol-sensitive upstream activation sequence in yeast. A cis-regulatory element responsible for inositol-choline mediated regulation of phospholipid biosynthesis. J Biol Chem 1995, 270: 25087-95. 10.1074\u002Fjbc.270.42.25087.\nGreenberg ML, Reiner B, Henry SA: Regulatory mutations of inositol biosynthesis in yeast: isolation of inositol-excreting mutants. Genetics 1982, 100: 19-33.\nAshburner BP, Lopes JM: Regulation of yeast phospholipid biosynthetic gene expression in response to inositol involves two superimposed mechanisms. Proc Natl Acad Sci USA 1995, 92: 9722-6. 10.1073\u002Fpnas.92.21.9722.\nKohno O, Normington K, Sambrook J, Gething MJ, Mori K: The promoter region of the yeast KAR2 (BiP) gene contains a regulatory domain that responds to the presence of unfolded proteins in the endoplasmic reticulum. Mol Cell Biol 1993, 13: 877-890.\nGuo S, Stolz LE, Lemrow SM, York JD: SAC1-like domains of yeast SAC1, INP52, and INP53 and of human synaptojanin encode polyphosphoinositide phosphatases. J Biol Chem 1999, 274: 12990-5. 10.1074\u002Fjbc.274.19.12990.\nAudhya A, Foti M, Emr SD: Distinct roles for the yeast phosphatidylinositol 4-kinases, Stt4p and Pik1p, in secretion, cell growth, and organelle membrane dynamics. Mol Biol Cell 2000, 11: 2673-89.\nKonrad G, Schlecker T, Faulhammer F, Mayinger P: Retention of the yeast Sac1p phosphatase in the endoplasmic reticulum causes distinct changes in cellular phosphoinositide levels and stimulates microsomal ATP transport. J Biol Chem 2002, 277: 10547-54. 10.1074\u002Fjbc.M200090200.\nFaulhammer F, S Kanjilal-Kolar, Knodler A, Lo J, Lee Y, Konrad G, Mayinger P: Growth Control of Golgi Phosphoinositides by Reciprocal Localization of Sac1 Lipid Phosphatase and Pik1 4-Kinase. Traffic 2007.\nMori K, Ogawa N, Kawahara T, Yanagi H, Yura T: Palindrome with spacer of one nucleotide is characteristic of the cis-acting unfolded protein response element in Saccharomyces cerevisiae. J Biol Chem 1998, 273: 9912-20. 10.1074\u002Fjbc.273.16.9912.\nBunce MW, Bergendahl K, Anderson RA: Nuclear PI(4,5)P(2): a new place for an old signal. Biochim Biophys Acta 2006, 1761: 560-9.\nDeleris P, Gayral S, Breton-Douillon M: Nuclear Ptdlns(3,4,5)P3 signaling: an ongoing story. J Cell Biochem 2006, 98: 469-85. 10.1002\u002Fjcb.20695.\nHomma K, Terui S, Minemura M, Qadota H, Anraku Y, Kanaho Y, Ohya Y: Phosphatidylinositol-4-phosphate 5-kinase localized on the plasma membrane is essential for yeast cell morphogenesis. J Biol Chem 1998, 273: 15779-86. 10.1074\u002Fjbc.273.25.15779.\nDesrivieres S, Cooke FT, Parker PJ, Hall MN: MSS4, a phosphatidylinositol-4-phosphate 5-kinase required for organization of the actin cytoskeleton in Saccharomyces cerevisiae. J Biol Chem 1998, 273: 15787-93. 10.1074\u002Fjbc.273.25.15787.\nFlick JS, Thorner J: Genetic and biochemical characterization of a phosphatidylinositol-specific phospholipase C in Saccharomyces cerevisiae. Mol Cell Biol 1993, 13: 5861-76.\nYork JD, Odom AR, Murphy R, Ives EB, Wente SR: A phospholipase C-dependent inositol polyphosphate kinase pathway required for efficient messenger RNA export. Science 1999, 285: 96-100. 10.1126\u002Fscience.285.5424.96.\nOdom AR, Stahlberg A, Wente SR, York JD: A role for nuclear inositol 1,4,5-trisphosphate kinase in transcriptional control. Science 2000, 287: 2026-9. 10.1126\u002Fscience.287.5460.2026.\nSikorski RS, Hieter P: A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 1989, 122: 19-27.\nHarlow E, Lane D: Antibodies: A laboratory manual. Cold Spring Harbor Laboratory; 1988.\nSchorr M, Then A, Tahirovic S, Hug N, Mayinger P: The phosphoinositide phosphatase Sac1p controls trafficking of the yeast Chs3p chitin synthase. 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KA, Park S, Lee SH, Kim JH, Lee JS. Comparison of circulating plasma DNA levels between lung cancer patients and healthy controls. J Mol Diagn. 2009;11:182–5.",{"doi":791},"10.2353\u002Fjmoldx.2009.080098",{"id":18,"text":793,"url":18,"identifiers":794},"Jung K, Fleischhacker M, Rabien A. Cell-free DNA in the blood as a solid tumor biomarker—a critical appraisal of the literature. Clin Chim Acta. 2010;411:1611–24.",{"doi":795},"10.1016\u002Fj.cca.2010.07.032",{"id":18,"text":797,"url":18,"identifiers":798},"Szpechcinski A, Chorostowska-Wynimko J, Struniawski R, Kupis W, Rudzinski P, Langfort R, et al. Cell-free DNA levels in plasma of patients with non-small-cell lung cancer and inflammatory lung disease. Br J Cancer. 2015;28(113):476–83.",{"doi":799},"10.1038\u002Fbjc.2015.225",{"id":18,"text":801,"url":18,"identifiers":802},"Tissot C, Toffart AC, Villar S, Souquet PJ, Merle P, Moro-Sibilot D, et al. Circulating free DNA concentration is an independent prognostic biomarker in lung cancer. Eur Respir J. 2015;46:1773–80.",{"doi":803},"10.1183\u002F13993003.00676-2015",{"id":18,"text":805,"url":18,"identifiers":806},"Oakes CC, La Salle S, Robaire B, Trasler JM. Evaluation of a quantitative DNA methylation analysis technique using methylation-sensitive\u002Fdependent restriction enzymes and real-time PCR. Epigenetics. 2006;1:146–52.",{"doi":807},"10.4161\u002Fepi.1.3.3392",{"id":18,"text":809,"url":18,"identifiers":810},"Zhang Y, Rohde C, Tierling S, Stamerjohanns H, Reinhardt R, Walter J, et al. DNA methylation analysis by bisulfite conversion, cloning, and sequencing of individual clones. Methods Mol Biol. 2009;507:177–87.",{"doi":811},"10.1007\u002F978-1-59745-522-0_14",{"id":18,"text":813,"url":18,"identifiers":814},"Paliwal A, Vaissiere T, Herceg Z. Quantitative detection of DNA methylation states in minute amounts of DNA from body fluids. Methods. 2010;52:242–7.",{"doi":815},"10.1016\u002Fj.ymeth.2010.03.008",{"id":18,"text":817,"url":18,"identifiers":818},"Wang T, Guan W, Lin J, Boutaoui N, Canino G, Luo J, et al. A systematic study of normalization methods for Infinium 450 K methylation data using whole-genome bisulfite sequencing data. Epigenetics. 2015;10:662–9.",{"doi":819},"10.1080\u002F15592294.2015.1057384",{"id":18,"text":821,"url":18,"identifiers":822},"Tanaka K, Okamoto A. Degradation of DNA by bisulfite treatment. Bioorg Med Chem Lett. 2007;17:1912–5.",{"doi":823},"10.1016\u002Fj.bmcl.2007.01.040",{"id":18,"text":825,"url":18,"identifiers":826},"Grunau C, Clark SJ, Rosenthal A. Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res. 2001;29(13):E65.",{"doi":827},"10.1093\u002Fnar\u002F29.13.e65",{"id":18,"text":829,"url":18,"identifiers":830},"Mill J, Petronis A. Profiling DNA methylation from small amounts of genomic DNA starting material: efficient sodium bisulfite conversion and subsequent whole-genome amplification. Methods Mol Biol. 2009;507:371–81.",{"doi":831},"10.1007\u002F978-1-59745-522-0_27",{"id":18,"text":833,"url":18,"identifiers":834},"Munson K, Clark J, Lamparska-Kupsik K, Smith SS. Recovery of bisulfite-converted genomic sequences in the methylation-sensitive ddPCR. Nucleic Acids Res. 2007;35:2893–903.",{"doi":835},"10.1093\u002Fnar\u002Fgkm055",{"id":18,"text":837,"url":18,"identifiers":838},"Jahr S, Hentze H, Englisch S, Hardt D, Fackelmayer FO, Hesch RD, et al. DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells. Cancer Res. 2001;61:1659–65.",{},{"id":18,"text":840,"url":18,"identifiers":841},"Hayatsu H, Negishi K, Shiraishi M. DNA methylation analysis: speedup of bisulfate-mediated deamination of cytosine in the genomic sequencing procedure. Proc Jpn Acad Ser B. 2004;80:189–94.",{"doi":842},"10.2183\u002Fpjab.80.189",{"id":18,"text":844,"url":18,"identifiers":845},"Shiraishi M, Hayatsu H. High-speed conversion of cytosine to uracil in bisulfite genomic sequencing analysis of DNA methylation. DNA Res. 2004;11:409–15.",{"doi":846},"10.1093\u002Fdnares\u002F11.6.409",{"id":18,"text":848,"url":18,"identifiers":849},"Genereux DP, Johnson WC, Burden AF, Stoger R, Laird CD. Errors in the bisulfite conversion of DNA: modulating inappropriate and failed conversion frequencies. Nucleic Acids Res. 2008;36:e150.",{"doi":850},"10.1093\u002Fnar\u002Fgkn691",{"id":18,"text":852,"url":18,"identifiers":853},"Vaissière T, Cuenin C, Paliwal A, Vineis P, Hoek G, Krzyzanowski M, et al. Quantitative analysis of DNA methylation after whole bisulfitome amplification of a minute amount of DNA from body fluids. Epigenetics. 2009;4:221–30.",{"doi":854},"10.4161\u002Fepi.8833",{"id":18,"text":856,"url":18,"identifiers":857},"Rajput SK, Kumar S, Dave VP, Rajput A, Pandey HP, Datta TK. An improved method of bisulfite treatment and purification to study precise DNA methylation from as little as 10 pg DNA. Appl Biochem Biotechnol. 2012;168(4):797–804.",{"doi":858},"10.1007\u002Fs12010-012-9820-7",{"id":18,"text":860,"url":18,"identifiers":861},"Parsons HA, Beaver JA, Park BH. Circulating plasma tumor DNA. Adv Exp Med Biol. 2016;882:259–76.",{"doi":862},"10.1007\u002F978-3-319-22909-6_11",{"id":18,"text":864,"url":18,"identifiers":865},"Hudecova I. Digital PCR analysis of circulating nucleic acids. Clin Biochem. 2015;48:948–56.",{"doi":866},"10.1016\u002Fj.clinbiochem.2015.03.015",{"id":18,"text":868,"url":18,"identifiers":869},"Huggett JF, Cowen S, Foy CA. Considerations for digital PCR as an accurate molecular diagnostic tool. Clin Chem. 2015;61:79–88.",{"doi":870},"10.1373\u002Fclinchem.2014.221366",{"id":18,"text":872,"url":18,"identifiers":873},"Day E, Dear PH, McCaughan F. Digital PCR strategies in the development and analysis of molecular biomarkers for personalized medicine. Methods. 2013;59:101–7.",{"doi":874},"10.1016\u002Fj.ymeth.2012.08.001",{"id":18,"text":876,"url":18,"identifiers":877},"Pedersen IS, Krarup HB, Thorlacius-Ussing O, Madsen PH. High recovery of cell-free methylated DNA based on a rapid bisulfite-treatment protocol. BMC Mol Biol. 2012;13:12.",{"doi":878},"10.1186\u002F1471-2199-13-12",{"id":18,"text":880,"url":18,"identifiers":881},"Dammann R, Yang G, Pfeifer GP. Hyper-methylation of the CpG island of Ras association domain family 1A (RASSF1A), a putative tumor suppressor gene from the 3p21.3 locus, occurs in a large percentage of human breast cancers. Cancer Res. 2001;61:3105–9.",{},{"id":883,"createTime":884,"updateTime":885,"relativeEntities":886,"slug":887,"properties":888,"entityType":143,"verifyStatus":296,"verifyTime":885,"verifyNote":297,"syncStatus":17,"languages":18,"translateLanguages":18,"viewCount":19,"primaryUrl":897,"fullTextUrl":18,"authors":898,"publicationType":251,"publisherRelationship":1011,"citationCount":18,"citationInfo":18,"publishDate":1037,"publishYear":1038,"citationAnalyzeStatus":17,"lastCitationAnalyze":18,"indexDatabases":18,"openAccess":18,"references":18,"isForceReanalyzing":280},"6697bf78-d0ef-43b8-9b71-1eab9cae285a","2024-01-09T22:07:33.523+00:00","2025-01-14T23:56:34.084+00:00",[],"Flexible-promoter-architecture-requirements-for-coactivator-recruitment",{"references":889,"abstract":891,"title":893,"doi":895},{"VOID":890},"Carey M: The enhanceosome and transcriptional synergy. Cell. 1998, 92: 5-8. 10.1016\u002FS0092-8674(00)80893-4\nMerika M, Thanos D: Enhanceosomes. 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Science. 2003, 301: 71-76. 10.1126\u002Fscience.1084337",{"EN":892},"The spatial organization of transcription factor binding sites in regulatory DNA, and the composition of intersite sequences, influences the assembly of the multiprotein complexes that regulate RNA polymerase recruitment and thereby affects transcription. We have developed a genetic approach to investigate how reporter gene transcription is affected by varying the spacing between transcription factor binding sites. We characterized the components of promoter architecture that govern the yeast transcription factors Cbf1 and Met31\u002F32, which bind independently, but collaboratively recruit the coactivator Met4. A Cbf1 binding site was required upstream of a Met31\u002F32 binding site for full reporter gene expression. Distance constraints on coactivator recruitment were more flexible than those for cooperatively binding transcription factors. Distances from 18 to 50 bp between binding sites support efficient recruitment of Met4, with only slight modulation by helical phasing. Intriguingly, we found that certain sequences located between the binding sites abolished gene expression. These results yield insight to the influence of both binding site architecture and local DNA flexibility on gene expression, and can be used to refine computational predictions of gene expression from promoter sequences. In addition, our approach can be applied to survey promoter architecture requirements for arbitrary combinations of transcription factor binding sites.",{"EN":894},"Flexible promoter architecture requirements for coactivator recruitment",{"VOID":896},"10.1186\u002F1471-2199-7-16","https:\u002F\u002Fbmcmolbiol.biomedcentral.com\u002Farticles\u002F10.1186\u002F1471-2199-7-16",[899,926,941,974,996],{"id":900,"sortIndex":77,"researcher":18,"roles":901,"affiliations":902,"properties":923},"6bbc9ece-27ac-41e4-8ec7-f9082c9c6f00",[150],[903,915],{"id":904,"sortIndex":77,"affiliation":905,"properties":914},"55dc701b-33ed-4f12-ba33-fe8bcb91bab9",{"id":906,"createTime":907,"updateTime":908,"relativeEntities":909,"slug":910,"properties":911,"entityType":39,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"syncStatus":17,"languages":18,"translateLanguages":18,"viewCount":19},"209d64d0-16a2-43e4-8ec2-ee3a1b2f5038","2024-04-11T18:04:07.050+00:00","2024-09-03T01:31:47.216+00:00",[],"Affymetrix-Santa-Clara-USA",{"title":912},{"EN":913},"Affymetrix, Santa Clara, 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K, Montell C: TRP channels. Annu Rev Biochem. 2007, 76: 387-417. 10.1146\u002Fannurev.biochem.75.103004.142819\nDamann N, Voets T, Nilius B: TRPs in our senses. Curr Biol. 2008, 18 (18): R880-889. 10.1016\u002Fj.cub.2008.07.063\nBeech DJ: TRPC1: store-operated channel and more. Pflugers Arch. 2005, 451 (1): 53-60. 10.1007\u002Fs00424-005-1441-3\nRychkov G, Barritt GJ: TRPC1 Ca2+-permeable channels in animal cells. Handb Exp Pharmacol. 2007, 23-52. 179,\nZitt C, Zobel A, Obukhov AG, Harteneck C, Kalkbrenner F, Luckhoff A, Schultz G: Cloning and functional expression of a human Ca2+-permeable cation channel activated by calcium store depletion. Neuron. 1996, 16 (6): 1189-1196. 10.1016\u002FS0896-6273(00)80145-2\nMa X, Cao J, Luo J, Nilius B, Huang Y, Ambudkar IS, Yao X: Depletion of intracellular Ca2+ stores stimulates the translocation of vanilloid transient receptor potential 4-c1 heteromeric channels to the plasma membrane. Arterioscler Thromb Vasc Biol. 2010, 30 (11): 2249-2255. 10.1161\u002FATVBAHA.110.212084\nAl-Shawaf E, Naylor J, Taylor H, Riches K, Milligan CJ, O'Regan D, Porter KE, Li J, Beech DJ: Short-term stimulation of calcium-permeable transient receptor potential canonical 5-containing channels by oxidized phospholipids. Arterioscler Thromb Vasc Biol. 2010, 30 (7): 1453-1459. 10.1161\u002FATVBAHA.110.205666\nLiu X, Cheng KT, Bandyopadhyay BC, Pani B, Dietrich A, Paria BC, Swaim WD, Beech D, Yildrim E, Singh BB, Birnbaumer L, Ambudkar IS: Attenuation of store-operated Ca2+ current impairs salivary gland fluid secretion in TRPC1(-\u002F-) mice. Proc Natl Acad Sci USA. 2007, 104 (44): 17542-17547. 10.1073\u002Fpnas.0701254104\nXu SZ, Muraki K, Zeng F, Li J, Sukumar P, Shah S, Dedman AM, Flemming PK, McHugh D, Naylor J, Cheong A, Bateson AN, Munsch CM, Porter KE, Beech DJ: A sphingosine-1-phosphate-activated calcium channel controlling vascular smooth muscle cell motility. Circ Res. 2006, 98 (11): 1381-1389. 10.1161\u002F01.RES.0000225284.36490.a2\nXu SZ, Sukumar P, Zeng F, Li J, Jairaman A, English A, Naylor J, Ciurtin C, Majeed Y, Milligan CJ, Bahnasi YM, Al-Shawaf E, Porter KE, Jiang LH, Emery P, Sivaprasadarao A, Beech DJ: TRPC channel activation by extracellular thioredoxin. Nature. 2008, 451 (7174): 69-72. 10.1038\u002Fnature06414\nSeth M, Zhang ZS, Mao L, Graham V, Burch J, Stiber J, Tsiokas L, Winn M, Abramowitz J, Rockman HA, Birnbaumer L, Rosenberg P: TRPC1 channels are critical for hypertrophic signaling in the heart. Circ Res. 2009, 105 (10): 1023-1030. 10.1161\u002FCIRCRESAHA.109.206581\nKumar B, Dreja K, Shah SS, Cheong A, Xu SZ, Sukumar P, Naylor J, Forte A, Cipollaro M, McHugh D, Kingston PA, Heagerty AM, Munsch CM, Bergdahl A, Hultgårdh-Nilsson A, Gomez MF, Porter KE, Hellstrand P, Beech DJ: Upregulated TRPC1 channel in vascular injury in vivo and its role in human neointimal hyperplasia. Circ Res. 2006, 98 (4): 557-563. 10.1161\u002F01.RES.0000204724.29685.db\nTakahashi Y, Watanabe H, Murakami M, Ohba T, Radovanovic M, Ono K, Iijima T, Ito H: Involvement of transient receptor potential canonical 1 (TRPC1) in angiotensin II-induced vascular smooth muscle cell hypertrophy. Atherosclerosis. 2007, 195 (2): 287-296. 10.1016\u002Fj.atherosclerosis.2006.12.033\nLi J, Sukumar P, Milligan CJ, Kumar B, Ma ZY, Munsch CM, Jiang LH, Porter KE, Beech DJ: Interactions, functions, and independence of plasma membrane STIM1 and TRPC1 in vascular smooth muscle cells. Circ Res. 2008, 103 (8): e97-104. 10.1161\u002FCIRCRESAHA.108.182931\nEdwards JM, Neeb ZP, Alloosh MA, Long X, Bratz IN, Peller CR, Byrd JP, Kumar S, Obukhov AG, Sturek M: Exercise training decreases store-operated Ca2+ entry associated with metabolic syndrome and coronary atherosclerosis. Cardiovasc Res. 2010, 85 (3): 631-640. 10.1093\u002Fcvr\u002Fcvp308\nParia BC, Malik AB, Kwiatek AM, Rahman A, May MJ, Ghosh S, Tiruppathi C: Tumor necrosis factor-alpha induces nuclear factor-kappaB-dependent TRPC1 expression in endothelial cells. J Biol Chem. 2003, 278 (39): 37195-37203. 10.1074\u002Fjbc.M304287200\nWang J, Weigand L, Lu W, Sylvester JT, Semenza GL, Shimoda LA: Hypoxia inducible factor 1 mediates hypoxia-induced TRPC expression and elevated intracellular Ca2+ in pulmonary arterial smooth muscle cells. Circ Res. 2006, 98 (12): 1528-1537. 10.1161\u002F01.RES.0000227551.68124.98\nMorales S, Diez A, Puyet A, Camello PJ, Camello-Almaraz C, Bautista JM, Pozo MJ: Calcium controls smooth muscle TRPC gene transcription via the CaMK\u002Fcalcineurin-dependent pathways. Am J Physiol Cell Physiol. 2007, 292 (1): C553-563.\nSakura H, Ashcroft FM: Identification of four trp1 gene variants murine pancreatic beta-cells. Diabetologia. 1997, 40 (5): 528-532. 10.1007\u002Fs001250050711\nWes PD, Chevesich J, Jeromin A, Rosenberg C, Stetten G, Montell C: TRPC1, a human homolog of a Drosophila store-operated channel. Proc Natl Acad Sci USA. 1995, 92 (21): 9652-9656. 10.1073\u002Fpnas.92.21.9652\nYang M, Gupta A, Shlykov SG, Corrigan R, Tsujimoto S, Sanborn BM: Multiple Trp isoforms implicated in capacitative calcium entry are expressed in human pregnant myometrium and myometrial cells. Biol Reprod. 2002, 67 (3): 988-994. 10.1095\u002Fbiolreprod.102.004119\nHolbrook JA, Neu-Yilik G, Hentze MW, Kulozik AE: Nonsense-mediated decay approaches the clinic. Nat Genet. 2004, 36 (8): 801-808. 10.1038\u002Fng1403\nChang YF, Imam JS, Wilkinson MF: The nonsense-mediated decay RNA surveillance pathway. Annu Rev Biochem. 2007, 76: 51-74. 10.1146\u002Fannurev.biochem.76.050106.093909\nIsken O, Maquat LE: The multiple lives of NMD factors: balancing roles in gene and genome regulation. Nat Rev Genet. 2008, 9 (9): 699-712. 10.1038\u002Fnrg2402\nStalder L, Muhlemann O: The meaning of nonsense. Trends Cell Biol. 2008, 18 (7): 315-321. 10.1016\u002Fj.tcb.2008.04.005\nGong Q, Zhang L, Vincent GM, Horne BD, Zhou Z: Nonsense mutations in hERG cause a decrease in mutant mRNA transcripts by nonsense-mediated mRNA decay in human long-QT syndrome. Circulation. 2007, 116 (1): 17-24. 10.1161\u002FCIRCULATIONAHA.107.708818\nBaek D, Green P: Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing. Proc Natl Acad Sci USA. 2005, 102 (36): 12813-12818. 10.1073\u002Fpnas.0506139102\nLewis BP, Green RE, Brenner SE: Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc Natl Acad Sci USA. 2003, 100 (1): 189-192. 10.1073\u002Fpnas.0136770100\nCarrier L, Schlossarek S, Willis MS, Eschenhagen T: The ubiquitin-proteasome system and nonsense-mediated mRNA decay in hypertrophic cardiomyopathy. Cardiovasc Res. 2010, 85 (2): 330-338. 10.1093\u002Fcvr\u002Fcvp247\nGreen RE, Lewis BP, Hillman RT, Blanchette M, Lareau LF, Garnett AT, Rio DC, Brenner SE: Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes. Bioinformatics. 2003, 19 (Suppl 1): i118-121. 10.1093\u002Fbioinformatics\u002Fbtg1015\nZetoune AB, Fontaniere S, Magnin D, Anczukow O, Buisson M, Zhang CX, Mazoyer S: Comparison of nonsense-mediated mRNA decay efficiency in various murine tissues. BMC Genet. 2008, 9: 83-\nGardner LB: Nonsense-mediated RNA decay regulation by cellular stress: implications for tumorigenesis. Mol Cancer Res. 2010, 8 (3): 295-308. 10.1158\u002F1541-7786.MCR-09-0502\nMedghalchi SM, Frischmeyer PA, Mendell JT, Kelly AG, Lawler AM, Dietz HC: Rent1, a trans-effector of nonsense-mediated mRNA decay, is essential for mammalian embryonic viability. Hum Mol Genet. 2001, 10 (2): 99-105. 10.1093\u002Fhmg\u002F10.2.99\nAzzalin CM, Lingner J: The human RNA surveillance factor UPF1 is required for S phase progression and genome stability. Curr Biol. 2006, 16 (4): 433-439. 10.1016\u002Fj.cub.2006.01.018\nAngelini GD, Jeremy JY: Towards the treatment of saphenous vein bypass graft failure--a perspective of the Bristol Heart Institute. Biorheology. 2002, 39 (3-4): 491-499.\nChu X, Tong Q, Wozney J, Zhang W, Cheung JY, Conrad K, Mazack V, Stahl R, Barber DL, Miller BA: Identification of an N-terminal TRPC2 splice variant which inhibits calcium influx. Cell Calcium. 2005, 37 (2): 173-182. 10.1016\u002Fj.ceca.2004.08.005\nSatoh E, Ono K, Xu F, Iijima T: Cloning and functional expression of a novel splice variant of rat TRPC4. Circ J. 2002, 66 (10): 954-958. 10.1253\u002Fcircj.66.954\nXu XZ, Moebius F, Gill DL, Montell C: Regulation of melastatin, a TRP-related protein, through interaction with a cytoplasmic isoform. Proc Natl Acad Sci USA. 2001, 98 (19): 10692-10697. 10.1073\u002Fpnas.191360198\nZhang W, Chu X, Tong Q, Cheung JY, Conrad K, Masker K, Miller BA: A novel TRPM2 isoform inhibits calcium influx and susceptibility to cell death. J Biol Chem. 2003, 278 (18): 16222-16229. 10.1074\u002Fjbc.M300298200\nFountain SJ, Cheong A, Flemming R, Mair L, Sivaprasadarao A, Beech DJ: Functional up-regulation of KCNA gene family expression in murine mesenteric resistance artery smooth muscle. J Physiol. 2004, 556 (Pt 1): 29-42.\nBustin SA, Beaulieu JF, Huggett J, Jaggi R, Kibenge FS, Olsvik PA, Penning LC, Toegel S: MIQE precis: Practical implementation of minimum standard guidelines for fluorescence-based quantitative real-time PCR experiments. BMC Mol Biol. 2010, 11: 74- 10.1186\u002F1471-2199-11-74\nApplequist SE, Selg M, Raman C, Jack HM: Cloning and characterization of HUPF1, a human homolog of the Saccharomyces cerevisiae nonsense mRNA-reducing UPF1 protein. Nucleic Acids Res. 1997, 25 (4): 814-821. 10.1093\u002Fnar\u002F25.4.814",{"EN":1049},"Transient Receptor Potential Canonical 1 (TRPC1) is a widely-expressed mammalian cationic channel with functional effects that include stimulation of cardiovascular remodelling. The initial aim of this study was to investigate variation in TRPC1-encoding gene transcripts. Extensive TRPC1 transcript alternative splicing was observed, with exons 2, 3 and 5-9 frequently omitted, leading to variants containing premature termination codons. Consistent with the predicted sensitivity of such variants to nonsense-mediated decay (NMD) the variants were increased by cycloheximide. However it was notable that control of the variants by NMD was prominent in human embryonic kidney 293 cells but not human vascular smooth muscle cells. The cellular difference was attributed in part to a critical protein in NMD, up-frameshift-1 (UPF1), which was found to have low abundance in the vascular cells. Rescue of UPF1 by expression of exogenous UPF1 was found to suppress vascular smooth muscle cell proliferation. The data suggest: (i) extensive NMD-sensitive transcripts of TRPC1; (ii) inefficient clearance of aberrant transcripts and enhanced proliferation of vascular smooth muscle cells in part because of low UPF1 expression.",{"EN":1051},"TRPC1 transcript variants, inefficient nonsense-mediated decay and low up-frameshift-1 in vascular smooth muscle 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EM: The Pur protein family: clues to function from recent studies on cancer and AIDS. Anticancer research. 2003, 23 (3A): 2093-2100.\nVassilev L, Johnson EM: An initiation zone of chromosomal DNA replication located upstream of the c-myc gene in proliferating HeLa cells. Molecular and cellular biology. 1990, 10 (9): 4899-4904.\nBergemann AD, Ma ZW, Johnson EM: Sequence of cDNA comprising the human pur gene and sequence-specific single-stranded-DNA-binding properties of the encoded protein. Molecular and cellular biology. 1992, 12 (12): 5673-5682.\nBergemann AD, Johnson EM: The HeLa Pur factor binds single-stranded DNA at a specific element conserved in gene flanking regions and origins of DNA replication. Molecular and cellular biology. 1992, 12 (3): 1257-1265.\nDarbinian N, Gallia GL, Khalili K: Helix-destabilizing properties of the human single-stranded DNA- and RNA-binding protein Puralpha. Journal of cellular biochemistry. 2001, 80 (4): 589-595. 10.1002\u002F1097-4644(20010315)80:4\u003C589::AID-JCB1013>3.0.CO;2-0\nBecker NA, Kelm RJ, Vrana JA, Getz MJ, Maher LJ: Altered sensitivity to single-strand-specific reagents associated with the genomic vascular smooth muscle alpha-actin promoter during myofibroblast differentiation. The Journal of biological chemistry. 2000, 275 (20): 15384-15391. 10.1074\u002Fjbc.M909687199\nWortman MJ, Johnson EM, Bergemann AD: Mechanism of DNA binding and localized strand separation by Pur alpha and comparison with Pur family member, Pur beta. Biochimica et biophysica acta. 2005, 1743 (1-2): 64-78.\nShimotai Y, Minami H, Saitoh Y, Onodera Y, Mishima Y, Kelm RJ, Tsutsumi K: A binding site for Pur alpha and Pur beta is structurally unstable and is required for replication in vivo from the rat aldolase B origin. Biochemical and biophysical research communications. 2006, 340 (2): 517-525. 10.1016\u002Fj.bbrc.2005.12.032\nLiu H, Barr SM, Chu C, Kohtz DS, Kinoshita Y, Johnson EM: Functional interaction of Puralpha with the Cdk2 moiety of cyclin A\u002FCdk2. Biochemical and biophysical research communications. 2005, 328 (4): 851-857. 10.1016\u002Fj.bbrc.2005.01.038\nChen NN, Chang CF, Gallia GL, Kerr DA, Johnson EM, Krachmarov CP, Barr SM, Frisque RJ, Bollag B, Khalili K: Cooperative action of cellular proteins YB-1 and Pur alpha with the tumor antigen of the human JC polyomavirus determines their interaction with the viral lytic control element. Proceedings of the National Academy of Sciences of the United States of America. 1995, 92 (4): 1087-1091. 10.1073\u002Fpnas.92.4.1087\nDaniel DC, Kinoshita Y, Khan MA, Valle LD, Khalili K, Rappaport J, Johnson EM: Internalization of exogenous human immunodeficiency virus-1 protein, Tat, by KG-1 oligodendroglioma cells followed by stimulation of DNA replication initiated at the JC virus origin. DNA and cell biology. 2004, 23 (12): 858-867. 10.1089\u002Fdna.2004.23.858\nDaniel DC, Wortman MJ, Schiller RJ, Liu H, Gan L, Mellen JS, Chang CF, Gallia GL, Rappaport J, Khalili K: Coordinate effects of human immunodeficiency virus type 1 protein Tat and cellular protein Puralpha on DNA replication initiated at the JC virus origin. The Journal of general virology. 2001, 82 (Pt 7): 1543-1553.\nJohnson EM, Chen PL, Krachmarov CP, Barr SM, Kanovsky M, Ma ZW, Lee WH: Association of human Pur alpha with the retinoblastoma protein, Rb, regulates binding to the single-stranded DNA Pur alpha recognition element. The Journal of biological chemistry. 1995, 270 (41): 24352-24360. 10.1074\u002Fjbc.270.41.24352\nWang H, Wang M, Reiss K, Darbinian-Sarkissian N, Johnson EM, Iliakis G, Amini S, Khalili K, Rappaport J: Evidence for the Involvement of Puralpha in Response to DNA Replication Stress. Cancer Biol Ther. 2007, 6 (4):\nBarr SM, Johnson EM: Ras-induced colony formation and anchorage-independent growth inhibited by elevated expression of Puralpha in NIH3T3 cells. Journal of cellular biochemistry. 2001, 81 (4): 621-638. 10.1002\u002Fjcb.1099\nMuller-Tidow C, Ji P, Diederichs S, Potratz J, Baumer N, Kohler G, Cauvet T, Choudary C, van der Meer T, Chan WY: The cyclin A1-CDK2 complex regulates DNA double-strand break repair. Molecular and cellular biology. 2004, 24 (20): 8917-8928. 10.1128\u002FMCB.24.20.8917-8928.2004\nLezon-Geyda K, Najfeld V, Johnson EM: Deletions of PURA, at 5q31, and PURB, at 7p13, in myelodysplastic syndrome and progression to acute myelogenous leukemia. Leukemia. 2001, 15 (6): 954-962. 10.1038\u002Fsj.leu.2402108\nKimura K, Wakamatsu A, Suzuki Y, Ota T, Nishikawa T, Yamashita R, Yamamoto J, Sekine M, Tsuritani K, Wakaguri H: Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome research. 2006, 16 (1): 55-65. 10.1101\u002Fgr.4039406\nKhalili K, Del Valle L, Muralidharan V, Gault WJ, Darbinian N, Otte J, Meier E, Johnson EM, Daniel DC, Kinoshita Y: Puralpha is essential for postnatal brain development and developmentally coupled cellular proliferation as revealed by genetic inactivation in the mouse. Molecular and cellular biology. 2003, 23 (19): 6857-6875. 10.1128\u002FMCB.23.19.6857-6875.2003\nCampbell AE, Slater JS, Futch WS: Murine cytomegalovirus-induced suppression of antigen-specific cytotoxic T lymphocyte maturation. Virology. 1989, 173 (1): 268-275. 10.1016\u002F0042-6822(89)90243-2\nHanson LK, Slater JS, Cavanaugh VJ, Newcomb WW, Bolin LL, Nelson CN, Fetters LD, Tang Q, Brown JC, Maul GG: Murine cytomegalovirus capsid assembly is dependent on US22 family gene M140 in infected macrophages. Journal of virology. 2009, 83 (15): 7449-7456. 10.1128\u002FJVI.00325-09\nJohnson EM, Kinoshita Y, Weinreb DB, Wortman MJ, Simon R, Khalili K, Winckler B, Gordon J: Role of Pur alpha in targeting mRNA to sites of translation in hippocampal neuronal dendrites. Journal of neuroscience research. 2006, 83 (6): 929-943. 10.1002\u002Fjnr.20806\nNiwa H, Yamamura K, Miyazaki J: Efficient selection for high-expression transfectants with a novel eukaryotic vector. Gene. 1991, 108 (2): 193-199. 10.1016\u002F0378-1119(91)90434-D\nBasler CF, Mikulasova A, Martinez-Sobrido L, Paragas J, Muhlberger E, Bray M, Klenk HD, Palese P, Garcia-Sastre A: The Ebola virus VP35 protein inhibits activation of interferon regulatory factor 3. Journal of virology. 2003, 77 (14): 7945-7956. 10.1128\u002FJVI.77.14.7945-7956.2003\nKinoshita Y, Johnson EM: Site-specific loading of an MCM protein complex in a DNA replication initiation zone upstream of the c-MYC gene in the HeLa cell cycle. The Journal of biological chemistry. 2004, 279 (34): 35879-35889. 10.1074\u002Fjbc.M401640200\nAltschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. Journal of molecular biology. 1990, 215 (3): 403-410.\nMuralidharan V, Cort L, Meier E, Blankenhorn EP, Khalili K: Molecular characterization and chromosomal localization of mouse Puralpha gene. Journal of cellular biochemistry. 2000, 77 (1): 1-5. 10.1002\u002F(SICI)1097-4644(20000401)77:1\u003C1::AID-JCB1>3.0.CO;2-L\nMuralidharan V, Sweet T, Nadraga Y, Amini S, Khalili K: Regulation of Puralpha gene transcription: evidence for autoregulation of Puralpha promoter. Journal of cellular physiology. 2001, 186 (3): 406-413. 10.1002\u002F1097-4652(2000)9999:999\u003C000::AID-JCP1039>3.0.CO;2-P\nNguyen H, Hiscott J, Pitha PM: The growing family of interferon regulatory factors. Cytokine & growth factor reviews. 1997, 8 (4): 293-312.\nDeFilippis VR: Induction and evasion of the type I interferon response by cytomegaloviruses. Advances in experimental medicine and biology. 2007, 598: 309-324. full_text\nKhalili K, Brady J, Khoury G: Translational regulation of SV40 early mRNA defines a new viral protein. Cell. 1987, 48 (4): 639-645. 10.1016\u002F0092-8674(87)90242-X\nKhalili K, Feigenbaum L, Khoury G: Evidence for a shift in 5'-termini of early viral RNA during the lytic cycle of JC virus. Virology. 1987, 158 (2): 469-472. 10.1016\u002F0042-6822(87)90224-8\nKhalili K, Khoury G, Brady J: Spacing between simian virus 40 early transcriptional control sequences is important for regulation of early RNA synthesis and gene expression. Journal of virology. 1986, 60 (3): 935-942.\nKrachmarov CP, Chepenik LG, Barr-Vagell S, Khalili K, Johnson EM: Activation of the JC virus Tat-responsive transcriptional control element by association of the Tat protein of human immunodeficiency virus 1 with cellular protein Pur alpha. Proceedings of the National Academy of Sciences of the United States of America. 1996, 93 (24): 14112-14117. 10.1073\u002Fpnas.93.24.14112\nWhite MK, Johnson EM, Khalili K: Multiple roles for Puralpha in cellular and viral regulation. Cell cycle (Georgetown, Tex. 2009, 8 (3): 1-7.\nLiu H, Johnson EM: Distinct proteins encoded by alternative transcripts of the PURG gene, located contrapodal to WRN on chromosome 8, determined by differential termination\u002Fpolyadenylation. Nucleic acids research. 2002, 30 (11): 2417-2426. 10.1093\u002Fnar\u002F30.11.2417\nItoh H, Wortman MJ, Kanovsky M, Uson RR, Gordon RE, Alfano N, Johnson EM: Alterations in Pur(alpha) levels and intracellular localization in the CV-1 cell cycle. Cell Growth Differ. 1998, 9 (8): 651-665.\nKalejta RF, Bechtel JT, Shenk T: Human cytomegalovirus pp71 stimulates cell cycle progression by inducing the proteasome-dependent degradation of the retinoblastoma family of tumor suppressors. Molecular and cellular biology. 2003, 23 (6): 1885-1895. 10.1128\u002FMCB.23.6.1885-1895.2003\nKalejta RF, Shenk T: Proteasome-dependent, ubiquitin-independent degradation of the Rb family of tumor suppressors by the human cytomegalovirus pp71 protein. Proceedings of the National Academy of Sciences of the United States of America. 2003, 100 (6): 3263-3268. 10.1073\u002Fpnas.0538058100\nFeire AL, Koss H, Compton T: Cellular integrins function as entry receptors for human cytomegalovirus via a highly conserved disintegrin-like domain. Proceedings of the National Academy of Sciences of the United States of America. 2004, 101 (43): 15470-15475. 10.1073\u002Fpnas.0406821101\nChan G, Bivins-Smith ER, Smith MS, Smith PM, Yurochko AD: Transcriptome analysis reveals human cytomegalovirus reprograms monocyte differentiation toward an M1 macrophage. J Immunol. 2008, 181 (1): 698-711.\nStacey DW, Hitomi M, Kanovsky M, Gan L, Johnson EM: Cell cycle arrest and morphological alterations following microinjection of NIH3T3 cells with Pur alpha. Oncogene. 1999, 18 (29): 4254-4261. 10.1038\u002Fsj.onc.1202795\nBain M, Sinclair J: The S phase of the cell cycle and its perturbation by human cytomegalovirus. Reviews in medical virology. 2007, 17 (6): 423-434. 10.1002\u002Frmv.551\nKalejta RF, Shenk T: The human cytomegalovirus UL82 gene product (pp71) accelerates progression through the G1 phase of the cell cycle. Journal of virology. 2003, 77 (6): 3451-3459. 10.1128\u002FJVI.77.6.3451-3459.2003\nGrandvaux N, Servant MJ, tenOever B, Sen GC, Balachandran S, Barber GN, Lin R, Hiscott J: Transcriptional profiling of interferon regulatory factor 3 target genes: direct involvement in the regulation of interferon-stimulated genes. Journal of virology. 2002, 76 (11): 5532-5539. 10.1128\u002FJVI.76.11.5532-5539.2002\nCarney DN, Gazdar AF, Bepler G, Guccion JG, Marangos PJ, Moody TW, Zweig MH, Minna JD: Establishment and identification of small cell lung cancer cell lines having classic and variant features. Cancer research. 1985, 45 (6): 2913-2923.\nStrahl BD, Allis CD: The language of covalent histone modifications. Nature. 2000, 403 (6765): 41-45. 10.1038\u002F47412",{"EN":1289},"Purα is an evolutionarily conserved cellular protein participating in processes of DNA replication, transcription, and RNA transport; all involving binding to nucleic acids and altering conformation and physical positioning. The distinct but related roles of Purα suggest a need for expression regulated differently depending on intracellular and external signals. Here we report that human PURA (hPURA) transcription is regulated from three distinct and widely-separated transcription start sites (TSS). Each of these TSS is strongly homologous to a similar site in mouse chromosomal DNA. Transcripts from TSS I and II are characterized by the presence of large and overlapping 5'-UTR introns terminated at the same splice receptor site. Transfection of lung carcinoma cells with wild-type or mutated hPURA 5' upstream sequences identifies different regulatory elements. TSS III, located within 80 bp of the translational start codon, is upregulated by E2F1, CAAT and NF-Y binding elements. Transcription at TSS II is downregulated through the presence of adjacent consensus binding elements for interferon regulatory factors (IRFs). Chromatin immunoprecipitation reveals that IRF-3 protein binds hPURA promoter sequences at TSS II in vivo. By co-transfecting hPURA reporter plasmids with expression plasmids for IRF proteins we demonstrate that several IRFs, including IRF-3, down-regulate PURA transcription. Infection of NIH 3T3 cells with mouse cytomegalovirus results in a rapid decrease in levels of mPURA mRNA and Purα protein. The viral infection alters the degree of splicing of the 5'-UTR introns of TSS II transcripts. Results provide evidence for a novel mechanism of transcriptional control by multiple promoters used differently in various tissues and cells. Viral infection alters not only the use of PURA promoters but also the generation of different non-coding RNAs from 5'-UTRs of the resulting transcripts.",{"EN":1291},"Regulation of PURA gene transcription by three promoters generating distinctly spliced 5-prime leaders: a novel means of fine control over tissue specificity and viral signals",{"VOID":1293},"10.1186\u002F1471-2199-11-81","https:\u002F\u002Fbmcmolbiol.biomedcentral.com\u002Farticles\u002F10.1186\u002F1471-2199-11-81",[1296,1311,1348,1363,1375,1387,1399],{"id":1297,"sortIndex":74,"researcher":18,"roles":1298,"affiliations":1299,"properties":1308},"239bd68f-1fdc-441d-8e6b-25b5696e2567",[150],[1300],{"id":18,"sortIndex":19,"affiliation":1301,"properties":18},{"id":1302,"createTime":1303,"updateTime":1303,"relativeEntities":1304,"slug":18,"properties":1305,"entityType":39,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"syncStatus":17,"languages":18,"translateLanguages":18,"viewCount":19},"9481b74a-8cc3-4c79-959f-e008737f8e22","2024-02-09T10:12:54.802+00:00",[],{"title":1306},{"VI":1307},"Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, USA",{"title":1309},{"VI":1310},"Luis 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USA",{},{"id":1326,"sortIndex":74,"affiliation":1327,"properties":1334},"b1d0c73a-24b7-4b26-a329-33d432e01c3a",{"id":1328,"createTime":1329,"updateTime":1329,"relativeEntities":1330,"slug":18,"properties":1331,"entityType":39,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"syncStatus":17,"languages":18,"translateLanguages":18,"viewCount":19},"e0683cf4-ed2c-40ef-9cfc-dce30b3109df","2024-01-05T22:07:53.751+00:00",[],{"title":1332},{"VI":1333},"Global Health and Emerging Pathogens Institute, Mount Sinai School of Medicine, New York, 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de Fernandez MT, Hayward WS, August JT: Bacterial proteins required for replication of phage Q ribonucleic acid. Pruification and properties of host factor I, a ribonucleic acid-binding protein. J Biol Chem. 1972, 247 (3): 824-831.\nArluison V, Mura C, Guzman MR, Liquier J, Pellegrini O, Gingery M, Regnier P, Marco S: Three-dimensional structures of fibrillar Sm proteins: Hfq and other Sm-like proteins. J Mol Biol. 2006, 356 (1): 86-96. 10.1016\u002Fj.jmb.2005.11.010.\nSauter C, Basquin J, Suck D: Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli. Nucleic Acids Res. 2003, 31 (14): 4091-4098. 10.1093\u002Fnar\u002Fgkg480.\nVassilieva M, Garber MB: The regulatory role of the Hfq protein in bacterial cells. Mol Biol (Mosk). 2002, 36 (6): 970-977.\nValentin-Hansen P, Eriksen M, Udesen C: The bacterial Sm-like protein Hfq: a key player in RNA transactions. Mol Microbiol. 2004, 51 (6): 1525-1533. 10.1111\u002Fj.1365-2958.2003.03935.x.\nGeissmann TA, Touati D: Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator. EMBO J. 2004, 23 (2): 396-405. 10.1038\u002Fsj.emboj.7600058.\nMoller T, Franch T, Hojrup P, Keene DR, Bachinger HP, Brennan RG, Valentin-Hansen P: Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction. Mol Cell. 2002, 9 (1): 23-30. 10.1016\u002FS1097-2765(01)00436-1.\nZhang A, Wassarman KM, Rosenow C, Tjaden BC, Storz G, Gottesman S: Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol. 2003, 50 (4): 1111-1124. 10.1046\u002Fj.1365-2958.2003.03734.x.\nRasmussen AA, Eriksen M, Gilany K, Udesen C, Franch T, Petersen C, Valentin-Hansen P: Regulation of ompA mRNA stability: the role of a small regulatory RNA in growth phase-dependent control. Mol Microbiol. 2005, 58 (5): 1421-1429.\nUdekwu KI, Darfeuille F, Vogel J, Reimegard J, Holmqvist E, Wagner EG: Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA. Genes Dev. 2005, 19 (19): 2355-2366. 10.1101\u002Fgad.354405.\nFolichon M, Arluison V, Pellegrini O, Huntzinger E, Regnier P, Hajnsdorf E: The poly(A) binding protein Hfq protects RNA from RNase E and exoribonucleolytic degradation. Nucleic Acids Res. 2003, 31 (24): 7302-7310. 10.1093\u002Fnar\u002Fgkg915.\nAzam TA, Hiraga S, Ishihama A: Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid. Genes Cells. 2000, 5 (8): 613-626. 10.1046\u002Fj.1365-2443.2000.00350.x.\nAzam TA, Ishihama A: Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity. J Biol Chem. 1999, 274 (46): 33105-331013. 10.1074\u002Fjbc.274.46.33105.\nHajnsdorf E, Regnier P: Host factor Hfq of Escherichia coli stimulates elongation of poly(A) tails by poly(A) polymerase I. Proc Natl Acad Sci USA. 2000, 97 (4): 1501-1505. 10.1073\u002Fpnas.040549897.\nMohanty BK, Maples VF, Kushner SR: The Sm-like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli. Mol Microbiol. 2004, 54 (4): 905-920. 10.1111\u002Fj.1365-2958.2004.04337.x.\nYue D, Maizels N, Weiner AM: CCA-adding enzymes and poly(A) polymerases are all members of the same nucleotidyltransferase superfamily: characterization of the CCA-adding enzyme from the archaeal hyperthermophile Sulfolobus shibatae. RNA. 1996, 2 (9): 895-908.\nSchürer H, Schiffer S, Marchfelder A, Mörl M: This is the end: processing, editing and repair at the tRNA 3'-terminus. Biol Chem. 2001, 382 (8): 1147-1156. 10.1515\u002FBC.2001.144.\nBetat H, Rammelt C, Martin G, Mörl M: Exchange of Regions between Bacterial Poly(A) polymerase and CCA Adding Enzyme Generates Altered Specificities. Mol Cell. 2004, 15: 389-398. 10.1016\u002Fj.molcel.2004.06.026.\nReuven NB, Zhou Z, Deutscher MP: Functional overlap of tRNA nucleotidyltransferase, poly(A) polymerase I, and polynucleotide phosphorylase. J Biol Chem. 1997, 272 (52): 33255-33259. 10.1074\u002Fjbc.272.52.33255.\nHall KB, Sampson JR, Uhlenbeck OC, Redfield AG: Structure of an unmodified tRNA molecule. Biochemistry. 1989, 28 (14): 5794-5801. 10.1021\u002Fbi00440a014.\nRobertus JD, Ladner JE, Finch JT, Rhodes D, Brown RS, Clark BF, Klug A: Structure of yeast phenylalanine tRNA at 3 A resolution. Nature. 1974, 250 (467): 546-551. 10.1038\u002F250546a0.\nSampson JR, Uhlenbeck OC: Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro. Proc Natl Acad Sci USA. 1988, 85 (4): 1033-1037. 10.1073\u002Fpnas.85.4.1033.\nShi H, Moore PB: The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited. RNA. 2000, 6 (8): 1091-1105. 10.1017\u002FS1355838200000364.\nThomas BC, Chamberlain J, Engelke DR, Gegenheimer P: Evidence for an RNA-based catalytic mechanism in eukaryotic nuclear ribonuclease P. RNA. 2000, 6 (4): 554-562. 10.1017\u002FS1355838200991477.\nKhvorova A, Motorin Y, Wolfson AD: Pyrophosphate mediates the effect of certain tRNA mutations on aminoacylation of yeast tRNA(Phe). Nucleic Acids Res. 1999, 27 (22): 4451-4456. 10.1093\u002Fnar\u002F27.22.4451.\nDale T, Sanderson LE, Uhlenbeck OC: The affinity of elongation factor Tu for an aminoacyl-tRNA is modulated by the esterified amino acid. Biochemistry. 2004, 43 (20): 6159-6166. 10.1021\u002Fbi036290o.\nGreenblatt J, McLimont M, Hanly S: Termination of transcription by nusA gene protein of Escherichia coli. Nature. 1981, 292 (5820): 215-220. 10.1038\u002F292215a0.\nReuter K, Ficner R: Sequence analysis and overexpression of the Zymomonas mobilis tgt gene encoding tRNA-guanine transglycosylase: purification and biochemical characterization of the enzyme. J Bacteriol. 1995, 177 (18): 5284-5288.\nBuck AH, Kazantsev AV, Dalby AB, Pace NR: Structural perspective on the activation of RNAse P RNA by protein. Nature structural & molecular biology. 2005, 12 (11): 958-964.\nBalandina A, Claret L, Hengge-Aronis R, Rouviere-Yaniv J: The Escherichia coli histone-like protein HU regulates rpoS translation. Molecular microbiology. 2001, 39 (4): 1069-1079. 10.1046\u002Fj.1365-2958.2001.02305.x.\nBalandina A, Kamashev D, Rouviere-Yaniv J: The bacterial histone-like protein HU specifically recognizes similar structures in all nucleic acids. DNA, RNA, and their hybrids. J Biol Chem. 2002, 277 (31): 27622-27628. 10.1074\u002Fjbc.M201978200.\nMikulecky PJ, Kaw MK, Brescia CC, Takach JC, Sledjeski DD, Feig AL: Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs. Nature structural & molecular biology. 2004, 11 (12): 1206-1214. 10.1038\u002Fnsmb858.\nZiolkowska K, Derreumaux P, Folichon M, Pellegrini O, Regnier P, Boni IV, Hajnsdorf E: Hfq variant with altered RNA binding functions. Nucleic acids research. 2006, 34 (2): 709-720. 10.1093\u002Fnar\u002Fgkj464.\nSonnleitner E, Napetschnig J, Afonyushkin T, Ecker K, Vecerek B, Moll I, Kaberdin VR, Blasi U: Functional effects of variants of the RNA chaperone Hfq. Biochem Biophys Res Commun. 2004, 323 (3): 1017-1023. 10.1016\u002Fj.bbrc.2004.08.190.\nVecerek B, Moll I, Blasi U: Translational autocontrol of the Escherichia coli hfq RNA chaperone gene. RNA. 2005, 11 (6): 976-984. 10.1261\u002Frna.2360205.\nTsui HC, Leung HC, Winkler ME: Characterization of broadly pleiotropic phenotypes caused by an hfq insertion mutation in Escherichia coli K-12. Mol Microbiol. 1994, 13 (1): 35-49. 10.1111\u002Fj.1365-2958.1994.tb00400.x.\nMuffler A, Traulsen DD, Fischer D, Lange R, Hengge-Aronis R: The RNA-binding protein HF-I plays a global regulatory role which is largely, but not exclusively, due to its role in expression of the sigmaS subunit of RNA polymerase in Escherichia coli. J Bacteriol. 1997, 179 (1): 297-300.\nZhang A, Wassarman KM, Ortega J, Steven AC, Storz G: The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol Cell. 2002, 9 (1): 11-22. 10.1016\u002FS1097-2765(01)00437-3.\nFolichon M, Allemand F, Regnier P, Hajnsdorf E: Stimulation of poly(A) synthesis by Escherichia coli poly(A)polymerase I is correlated with Hfq binding to poly(A) tails. The FEBS journal. 2005, 272 (2): 454-463. 10.1111\u002Fj.1742-4658.2004.04485.x.\nLe Derout J, Folichon M, Briani F, Deho G, Regnier P, Hajnsdorf E: Hfq affects the length and the frequency of short oligo(A) tails at the 3' end of Escherichia coli rpsO mRNAs. Nucleic Acids Res. 2003, 31 (14): 4017-4023. 10.1093\u002Fnar\u002Fgkg456.\nLease RA, Woodson SA: Cycling of the Sm-like protein Hfq on the DsrA small regulatory RNA. J Mol Biol. 2004, 344 (5): 1211-1223. 10.1016\u002Fj.jmb.2004.10.006.\nZhu L, Deutscher MP: tRNA nucleotidyltransferase is not essential for Escherichia coli viability. EMBO J. 1987, 6 (8): 2473-2477.\nKufel J, Allmang C, Verdone L, Beggs JD, Tollervey D: Lsm proteins are required for normal processing of pre-tRNAs and their efficient association with La-homologous protein Lhp1p. Mol Cell Biol. 2002, 22 (14): 5248-5256. 10.1128\u002FMCB.22.14.5248-5256.2002.\nMörl M, Lizano E, Willkomm DK, Hartmann RK: Production of RNAs with Homogeneous 5' and 3' Ends. Handbook of RNA Biochemistry. Edited by: Hartmann RK, Bindereif A, Schön A, Westhof E. 2005, Weinheim , Wiley-VCH, 1: 22-35.",{"EN":1457},"The bacterial Sm-like protein Hfq is known as an important regulator involved in many reactions of RNA metabolism. A prominent function of Hfq is the stimulation of RNA polyadenylation catalyzed by E. coli poly(A) polymerase I (PAP). As a member of the nucleotidyltransferase superfamily, this enzyme shares a high sequence similarity with an other representative of this family, the tRNA nucleotidyltransferase that synthesizes the 3'-terminal sequence C-C-A to all tRNAs (CCA-adding enzyme). Therefore, it was assumed that Hfq might not only influence the poly(A) polymerase in its specific activity, but also other, similar enzymes like the CCA-adding enzyme. Based on the close evolutionary relation of these two nucleotidyltransferases, it was tested whether Hfq is a specific modulator acting exclusively on PAP or whether it also influences the activity of the CCA-adding enzyme. The obtained data indicate that the reaction catalyzed by this enzyme is substantially accelerated in the presence of Hfq. Furthermore, Hfq binds specifically to tRNA transcripts, which seems to be the prerequisite for the observed effect on CCA-addition. The increase of the CCA-addition in the presence of Hfq suggests that this protein acts as a stimulating factor not only for PAP, but also for the CCA-adding enzyme. In both cases, Hfq interacts with RNA substrates, while a direct binding to the corresponding enzymes was not demonstrated up to now (although experimental data indicate a possible interaction of PAP and Hfq). So far, the basic principle of these stimulatory effects is not clear yet. In case of the CCA-adding enzyme, however, the presented data indicate that the complex between Hfq and tRNA substrate might enhance the product release from the enzyme.",{"EN":1459},"Hfq stimulates the activity of the CCA-adding enzyme",{"VOID":1461},"10.1186\u002F1471-2199-8-92","https:\u002F\u002Fbmcmolbiol.biomedcentral.com\u002Farticles\u002F10.1186\u002F1471-2199-8-92",[1464,1479,1494,1506,1518],{"id":1465,"sortIndex":74,"researcher":18,"roles":1466,"affiliations":1467,"properties":1476},"68be4dd9-5bd4-4ffb-a3ad-4fe8c892c0bc",[150],[1468],{"id":18,"sortIndex":19,"affiliation":1469,"properties":18},{"id":1470,"createTime":1471,"updateTime":1471,"relativeEntities":1472,"slug":18,"properties":1473,"entityType":39,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"syncStatus":17,"languages":18,"translateLanguages":18,"viewCount":19},"a6a80af7-9b0d-4f8d-b013-7726397bd206","2023-12-31T05:53:34.718+00:00",[],{"title":1474},{"VI":1475},"UPR 9073 CNRS conventionnée avec l'Université Paris 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Genes Dev 1996,10(23):3041-3050. 10.1101\u002Fgad.10.23.3041\nDoench JG, Petersen CP, Sharp PA: siRNAs can function as miRNAs. Genes Dev 2003,17(4):438-442. 10.1101\u002Fgad.1064703\nBentwich I: Prediction and validation of microRNAs and their targets. FEBS Lett 2005,579(26):5904-5910. 10.1016\u002Fj.febslet.2005.09.040\nBaroukh N, Ravier MA, Loder MK, Hill EV, Bounacer A, Scharfmann R, Rutter GA, Van Obberghen E: MicroRNA-124a regulates Foxa2 expression and intracellular signaling in pancreatic beta-cell lines. J Biol Chem 2007,282(27):19575-19588. 10.1074\u002Fjbc.M611841200\nKnosel T, Schluns K, Dietel M, Petersen I: Chromosomal alterations in lung metastases of colorectal carcinomas: associations with tissue specific tumor dissemination. 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Genes Chromosomes Cancer 2005,44(4):405-414. 10.1002\u002Fgcc.20253\nShachaf CM, Kopelman AM, Arvanitis C, Karlsson A, Beer S, Mandl S, Bachmann MH, Borowsky AD, Ruebner B, Cardiff RD, Yang Q, Bishop JM, Contag CH, Felsher DW: MYC inactivation uncovers pluripotent differentiation and tumour dormancy in hepatocellular cancer. Nature 2004,431(7012):1112-1117. 10.1038\u002Fnature03043\nPelengaris S, Khan M, Evan GI: Suppression of Myc-induced apoptosis in beta cells exposes multiple oncogenic properties of Myc and triggers carcinogenic progression. Cell 2002,109(3):321-334. 10.1016\u002FS0092-8674(02)00738-9\nSeger R, Krebs EG: The MAPK signaling cascade. Faseb J 1995,9(9):726-735.\nKerkhoff E, Houben R, Loffler S, Troppmair J, Lee JE, Rapp UR: Regulation of c-myc expression by Ras\u002FRaf signalling. Oncogene 1998,16(2):211-216. 10.1038\u002Fsj.onc.1201520\nFernandez PC, Frank SR, Wang L, Schroeder M, Liu S, Greene J, Cocito A, Amati B: Genomic targets of the human c-Myc protein. Genes Dev 2003,17(9):1115-1129. 10.1101\u002Fgad.1067003\nDang CV: c-Myc target genes involved in cell growth, apoptosis, and metabolism. Mol Cell Biol 1999,19(1):1-11.\nProchownik EV: c-Myc as a therapeutic target in cancer. Expert Rev Anticancer Ther 2004,4(2):289-302. 10.1586\u002F14737140.4.2.289\nPonzielli R, Katz S, Barsyte-Lovejoy D, Penn LZ: Cancer therapeutics: targeting the dark side of Myc. Eur J Cancer 2005,41(16):2485-2501. 10.1016\u002Fj.ejca.2005.08.017\nPesole G, Liuni S, Grillo G, Licciulli F, Mignone F, Gissi C, Saccone C: UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002. Nucleic Acids Res 2002,30(1):335-340. 10.1093\u002Fnar\u002F30.1.335\nPesole G, Liuni S, Grillo G, Ippedico M, Larizza A, Makalowski W, Saccone C: UTRdb: a specialized database of 5' and 3' untranslated regions of eukaryotic mRNAs. Nucleic Acids Res 1999,27(1):188-191. 10.1093\u002Fnar\u002F27.1.188\nPesole G, Liuni S, Grillo G, Saccone C: UTRdb: a specialized database of 5'- and 3'-untranslated regions of eukaryotic mRNAs. Nucleic Acids Res 1998,26(1):192-195. 10.1093\u002Fnar\u002F26.1.192\nMignone F, Grillo G, Licciulli F, Iacono M, Liuni S, Kersey PJ, Duarte J, Saccone C, Pesole G: UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res 2005, (33 Database):D141-146.\nRusinov V, Baev V, Minkov IN, Tabler M: MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence. Nucleic Acids Res 2005, (33 Web Server):W696-700. 10.1093\u002Fnar\u002Fgki364\nGriffiths-Jones S: The microRNA Registry. Nucleic Acids Res 2004, (32 Database):D109-111. 10.1093\u002Fnar\u002Fgkh023\nKalantidis K, Psaradakis S, Tabler M, Tsagris M: The occurrence of CMV-specific short Rnas in transgenic tobacco expressing virus-derived double-stranded RNA is indicative of resistance to the virus. Mol Plant Microbe Interact 2002,15(8):826-833. 10.1094\u002FMPMI.2002.15.8.826",{"EN":1567},"MicroRNAs (miRNAs) are one of the most abundant groups of regulatory genes in multicellular organisms, playing important roles in many fundamental cellular processes. More than four hundred miRNAs have been identified in humans and the deregulation of miRNA expression has been also shown in many cancers. Despite the postulated involvement of miRNAs in tumourigenesis, there are only a few examples where an oncogene or a tumour suppressor has been identified as a miRNA target. Here, we present an in silico analysis of potential miRNA- oncogene interactions. Moreover, we have tested the validity of two possible interactions of miRNAs with genes related to cancer. We present evidence for the down-regulation of c-MYC, one of the most potent and frequently deregulated oncogenes, by let-7 miRNA, via the predicted binding site in the 3'UTR, and verify the suppression of BCL-2 by miR16. In this work both bioinformatic and experimental approaches for the prediction and validation of possible targets for miRNAs have been used. 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