Discovery of SMAD4 promoters, transcription factor binding sites and deletions in juvenile polyposis patients

Daniel Calva; Fadi S Dahdaleh; George Woodfield; Ronald J Weigel; Jennifer C Carr; Sathivel Chinnathambi; James R Howe

doi:10.1093/nar/gkr091

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Discovery of SMAD4 promoters, transcription factor binding sites and deletions in juvenile polyposis patients

Journal article

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Discovery of SMAD4 promoters, transcription factor binding sites and deletions in juvenile polyposis patients

Daniel Calva, Fadi S Dahdaleh, George Woodfield, Ronald J Weigel, Jennifer C Carr, Sathivel Chinnathambi and James R Howe

Nucleic acids research, Vol.39(13), pp.5369-5378

07/2011

DOI: 10.1093/nar/gkr091

PMCID: PMC3141234

PMID: 21421563

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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.

Gene Regulation, Chromatin and Epigenetics

Details

Title: Subtitle: Discovery of SMAD4 promoters, transcription factor binding sites and deletions in juvenile polyposis patients
Creators: Daniel Calva - Department of Surgery, Carver College of Medicine, University of Iowa Hospitals and Clinics, Iowa City, 52242-1086 IA, USA
Fadi S Dahdaleh - Department of Surgery, Carver College of Medicine, University of Iowa Hospitals and Clinics, Iowa City, 52242-1086 IA, USA
George Woodfield - Department of Surgery, Carver College of Medicine, University of Iowa Hospitals and Clinics, Iowa City, 52242-1086 IA, USA
Ronald J Weigel - Department of Surgery, Carver College of Medicine, University of Iowa Hospitals and Clinics, Iowa City, 52242-1086 IA, USA
Jennifer C Carr - Department of Surgery, Carver College of Medicine, University of Iowa Hospitals and Clinics, Iowa City, 52242-1086 IA, USA
Sathivel Chinnathambi - Department of Surgery, Carver College of Medicine, University of Iowa Hospitals and Clinics, Iowa City, 52242-1086 IA, USA
James R Howe - Department of Surgery, Carver College of Medicine, University of Iowa Hospitals and Clinics, Iowa City, 52242-1086 IA, USA
Resource Type: Journal article
Publication Details: Nucleic acids research, Vol.39(13), pp.5369-5378
DOI: 10.1093/nar/gkr091
PMID: 21421563
PMCID: PMC3141234
NLM abbreviation: Nucleic Acids Res
ISSN: 0305-1048
eISSN: 1362-4962
Publisher: Oxford University Press
Language: English
Date published: 07/2011
Academic Unit: Molecular Physiology and Biophysics; Anatomy and Cell Biology; Surgery; Biochemistry and Molecular Biology
Record Identifier: 9984051517102771

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