title: The promoter for intestinal cell kinase is head-to-head with F-Box 9 and contains functional sites for TCF7L2 and FOXA factors.
abstract: BACKGROUND
  Intestinal cell kinase (ICK; GeneID 22858) is a conserved MAPK and CDK-like kinase that is widely expressed in human tissues. Data from the Cancer Genome Anatomy Project indicated ICK mRNA is increased in cancer, and that its expression correlated with expression of mRNA for an uncharacterized F-box protein, FBX9 (GeneID: 26268). ICK and FBX9 genes are arranged head-to-head on opposite strands, with start sites for transcription separated by approximately 3.3 kb. We hypothesized ICK and FBX9 are potentially important genes in cancer controlled by a bidirectional promoter.
  
  
  RESULTS
  We assessed promoter activity of the intergenic region in both orientations in cancer cell lines derived from breast (AU565, SKBR3), colon (HCT-15, KM12), and stomach (AGS) cancers, as well as in embryonic human kidney (HEK293T) cells. The intergenic segment was active in both orientations in all of these lines, and ICK promoter activity was greater than FBX9 promoter activity. Results from deletions and truncations defined a minimal promoter for ICK, and revealed that repressors and enhancers differentially regulate ICK versus FBX9 promoter activity. The ICK promoter contains consensus motifs for several FOX-family transcription factors that align when mouse and human are compared using EMBOSS. FOXA1 and FOXA2 increase luciferase activity of a minimal promoter 10-20 fold in HEK293T cells. Consensus sites for TCF7L2 (TCF4) (Gene Id: 6934) are also present in both mouse and human. The expression of beta-catenin increased activity of the minimal promoter approximately 10 fold. ICK reference mRNAs (NM_014920.3, NM_016513) are expressed in low copy number and increased in some breast cancers, using a ten base tag 5'-TCAACCTTAT-3' specific for both ICK transcripts.
  
  
  CONCLUSIONS
  ICK and FBX9 are divergently transcribed from a bidirectional promoter that is GC-rich and contains a CpG island. A minimal promoter for ICK contains functional sites for beta-catenin/TCF7L2 and FOXA. These data are consistent with functions that have been proposed for ICK in development and in proliferation or survival of some breast and colon cancers.
authors.affiliation: Departments of Pharmacology and Internal Medicine, University of Virginia, 1300 Jefferson Park Avenue, Charlottesville, Virginia 22908, USA. tws7w@virginia.edu
authors.forename: Thomas W
authors.initials: TW
authors.lastname: Sturgill
authors.forename: Paul B
authors.initials: PB
authors.lastname: Stoddard
authors.forename: Steven M
authors.initials: SM
authors.lastname: Cohn
authors.forename: Marty W
authors.initials: MW
authors.lastname: Mayo
mesh_terms: D000818:Animals; D001483:Base Sequence; D015153:Blotting, Western; D045744:Cell Line, Tumor; D016384:Consensus Sequence; D017124:Conserved Sequence; D044783:F-Box Proteins / Q000235:genetics* / Q000378:metabolism; D051858:Forkhead Transcription Factors / Q000235:genetics* / Q000378:metabolism; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics*; D017346:Protein Serine-Threonine Kinases / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D051820:TCF Transcription Factors / Q000235:genetics* / Q000378:metabolism; D058118:Transcription Factor 7-Like 2 Protein; D051176:beta Catenin / Q000235:genetics / Q000378:metabolism
chemical_list: D044783:F-Box Proteins; C578379:Fbxo9 protein, human; D051858:Forkhead Transcription Factors; D051820:TCF Transcription Factors; C544894:TCF7L2 protein, human; C544895:Tcf7l2 protein, mouse; D058118:Transcription Factor 7-Like 2 Protein; D051176:beta Catenin; C097276:CILK1 protein, human; D017346:Protein Serine-Threonine Kinases
references.citation: Dev Cell. 2010 Feb 16;18(2):237-47
references.pmid: 20159594
references.citation: Mol Cell Biol. 2005 Jul;25(14):6047-64
references.pmid: 15988018
references.citation: Cell. 2007 Sep 21;130(6):1160
references.pmid: 17889656
references.citation: J Biol Chem. 2006 Jul 7;281(27):18307-16
references.pmid: 16684773
references.citation: Mol Cell Biol. 2008 Nov;28(21):6720-9
references.pmid: 18765639
references.citation: Cell. 2007 Oct 5;131(1):192
references.pmid: 17923097
references.citation: Nat Genet. 2008 Dec;40(12):1407-9
references.pmid: 18978787
references.citation: Mol Cell Biol. 2004 Jun;24(11):5028-38
references.pmid: 15143193
references.citation: J Biol Chem. 1998 May 29;273(22):14030-6
references.pmid: 9593754
references.citation: Nucleic Acids Res. 1995 Mar 25;23(6):901-9
references.pmid: 7731802
references.citation: Development. 1993 Dec;119(4):1301-15
references.pmid: 8306889
references.citation: Nucleic Acids Res. 1991 Aug 11;19(15):4139-45
references.pmid: 1870969
references.citation: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W249-52
references.pmid: 15215389
references.citation: J Biol Chem. 2000 Apr 28;275(17):12909-16
references.pmid: 10777590
references.citation: Genes Dev. 2007 Apr 1;21(7):848-61
references.pmid: 17403783
references.citation: Curr Opin Gastroenterol. 2003 Nov;19(6):583-90
references.pmid: 15703609
references.citation: Int J Cancer. 2009 Dec 1;125(11):2631-42
references.pmid: 19672860
references.citation: Am J Physiol Gastrointest Liver Physiol. 2009 Oct;297(4):G632-40
references.pmid: 19696144
references.citation: Nat Rev Mol Cell Biol. 2004 Sep;5(9):739-51
references.pmid: 15340381
references.citation: Mol Cell Biol. 2006 Nov;26(22):8639-54
references.pmid: 16954377
references.citation: Mol Carcinog. 1990;3(6):350-62
references.pmid: 1980588
references.citation: Mol Cell Biol. 2002 May;22(10):3276-80
references.pmid: 11971961
references.citation: J Biol Chem. 2008 Feb 8;283(6):3264-3271
references.pmid: 18056262
references.citation: Cell. 2002 Jun 28;109(7):807-9
references.pmid: 12110178
references.citation: Cell. 2002 Oct 18;111(2):241-50
references.pmid: 12408868
references.citation: Biochem Biophys Res Commun. 2001 Oct 12;287(5):1075-82
references.pmid: 11587531
references.citation: EMBO J. 2001 Nov 1;20(21):6028-36
references.pmid: 11689443
references.citation: Mol Cell Biol. 1993 Jul;13(7):4146-56
references.pmid: 8321219
references.citation: Mech Dev. 2000 Oct;97(1-2):157-60
references.pmid: 11025217
references.citation: Nat Genet. 1994 Mar;6(3):236-44
references.pmid: 8012384
references.citation: Oncogene. 1995 Dec 7;11(11):2187-95
references.pmid: 8570168
references.citation: J Biol Chem. 2004 Feb 13;279(7):6163-70
references.pmid: 14634024
references.citation: Chromosoma. 2009 Oct;118(5):549-65
references.pmid: 19506892
references.citation: Int J Dev Biol. 2009;53(2-3):335-54
references.pmid: 19412890
references.citation: J Biol Chem. 2003 Mar 14;278(11):9747-53
references.pmid: 12519780
references.citation: Mol Cell Biol. 2004 May;24(9):4065-74
references.pmid: 15082798
references.citation: Mol Biol Evol. 2009 Jun;26(6):1379-89
references.pmid: 19282513
references.citation: Nature. 2002 Jan 10;415(6868):180-3
references.pmid: 11805837
references.citation: Mol Cell Biol. 1994 Apr;14(4):2755-66
references.pmid: 8139574
references.citation: EMBO J. 1998 Nov 2;17(21):6135-43
references.pmid: 9799223
references.citation: Am J Hum Genet. 2009 Feb;84(2):134-47
references.pmid: 19185282
references.citation: J Cell Physiol. 2000 Apr;183(1):129-39
references.pmid: 10699974
references.citation: Mol Cell Biol. 1997 Mar;17(3):1626-41
references.pmid: 9032290
references.citation: Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):4262-6
references.pmid: 10759547
references.citation: Cancer Res. 2003 Dec 15;63(24):8634-47
references.pmid: 14695175
references.citation: Proc Natl Acad Sci U S A. 2004 Feb 3;101(5):1247-52
references.pmid: 14734805
references.citation: Biochem Biophys Res Commun. 1999 Dec 20;266(2):291-5
references.pmid: 10600495
references.citation: Science. 1995 Oct 20;270(5235):484-7
references.pmid: 7570003
references.citation: J Biol Chem. 2005 May 6;280(18):18095-107
references.pmid: 15741163
references.citation: J Biol Chem. 2003 May 23;278(21):18980-9
references.pmid: 12649266
references.citation: Mol Microbiol. 2005 Mar;55(5):1606-15
references.pmid: 15720564
references.citation: Biochem J. 2007 Aug 1;405(3):495-501
references.pmid: 17428197
references.citation: J Gen Virol. 1977 Jul;36(1):59-74
references.pmid: 886304
references.citation: Cancer Sci. 2009 Jan;100(1):47-53
references.pmid: 19018758
references.citation: Dev Cell. 2009 Apr;16(4):588-99
references.pmid: 19386267
references.citation: Cell Cycle. 2006 Mar;5(5):546-54
references.pmid: 16552187
references.citation: Mol Cell Biol. 2005 Nov;25(22):9910-9
references.pmid: 16260606
references.citation: Dev Biol. 2009 Jul 15;331(2):300-10
references.pmid: 19450575
references.citation: FEBS Lett. 2004 Aug 27;573(1-3):147-54
references.pmid: 15327990
references.citation: Mol Cell Biol. 2008 Apr;28(8):2732-44
references.pmid: 18268006
references.citation: Hepatology. 2006 Nov;44(5):1364
references.pmid: 17058235
references.citation: Mol Cell Biochem. 1994 Jul 13;136(1):49-57
references.pmid: 7854331
references.citation: Science. 1997 Mar 21;275(5307):1784-7
references.pmid: 9065401
references.citation: Genes Dev. 2004 Nov 1;18(21):2573-80
references.pmid: 15520277