title: Discovery of SMAD4 promoters, transcription factor binding sites and deletions in juvenile polyposis patients.
abstract: Inactivation of SMAD4 has been linked to several cancers and germline mutations cause juvenile polyposis (JP). We set out to identify the promoter(s) of SMAD4, evaluate their activity in cell lines and define possible transcription factor binding sites (TFBS). 5'-rapid amplification of cDNA ends (5'-RACE) and computational analyses were used to identify candidate promoters and corresponding TFBS and the activity of each was assessed by luciferase vectors in different cell lines. TFBS were disrupted by site-directed mutagenesis (SDM) to evaluate the effect on promoter activity. Four promoters were identified, two of which had significant activity in several cell lines, while two others had minimal activity. In silico analysis revealed multiple potentially important TFBS for each promoter. One promoter was deleted in the germline of two JP patients and SDM of several sites led to significant reduction in promoter activity. No mutations were found by sequencing this promoter in 65 JP probands. The predicted TFBS profiles for each of the four promoters shared few transcription factors in common, but were conserved across several species. The elucidation of these promoters and identification of TFBS has important implications for future studies in sporadic tumors from multiple sites, and in JP patients.
authors.affiliation: Department of Surgery, Carver College of Medicine, University of Iowa Hospitals and Clinics, Iowa City, 52242-1086 IA, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Calva
authors.forename: Fadi S
authors.initials: FS
authors.lastname: Dahdaleh
authors.forename: George
authors.initials: G
authors.lastname: Woodfield
authors.forename: Ronald J
authors.initials: RJ
authors.lastname: Weigel
authors.forename: Jennifer C
authors.initials: JC
authors.lastname: Carr
authors.forename: Sathivel
authors.initials: S
authors.lastname: Chinnathambi
authors.forename: James R
authors.initials: JR
authors.lastname: Howe
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002460:Cell Line; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation; D003850:Deoxyribonuclease I; D006801:Humans; D044483:Intestinal Polyposis / Q000235:genetics*; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D011401:Promoter Regions, Genetic; D012313:RNA / Q000032:analysis; D012326:RNA Splicing; D017384:Sequence Deletion; D051901:Smad4 Protein / Q000235:genetics*; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D051901:Smad4 Protein; D014157:Transcription Factors; D012313:RNA; D003850:Deoxyribonuclease I