Open AccessPromoter‐wide analysis of Smad4 binding sites in human epithelial cells
Author(s) -
Koinuma Daizo,
Tsutsumi Shuichi,
Kamimura Naoko,
Imamura Takeshi,
Aburatani Hiroyuki,
Miyazono Kohei
Publication year - 2009
Publication title -
cancer science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.035
H-Index - 141
eISSN - 1349-7006
pISSN - 1347-9032
DOI - 10.1111/j.1349-7006.2009.01299.x
Subject(s) - chromatin immunoprecipitation , biology , binding site , transcription factor , hacat , smad , carcinogenesis , promoter , smad2 protein , transforming growth factor beta , signal transduction , microbiology and biotechnology , gene , cancer research , gene expression , genetics , cell culture
Smad4, the common partner Smad, is a key molecule in transforming growth factor‐β (TGF‐β) family signaling. Loss of Smad4 expression is found in several types of cancer, including pancreatic cancer and colon cancer, and is related to carcinogenesis. Here we identified Smad4 binding sites in the promoter regions of over 25 500 known genes by chromatin immunoprecipitation on a microarray (ChIP‐chip) in HaCaT human keratinocytes. We identified 925 significant Smad4 binding sites. Approximately half of the identified sites overlapped the binding regions of Smad2 and Smad3 (Smad2/3, receptor‐regulated Smads in TGF‐β signaling), while the rest of the regions appeared dominantly occupied by Smad4 even when a different identification threshold for Smad2/3 binding regions was used. Distribution analysis showed that Smad4 was found in the regions relatively distant from the transcription start sites, while Smad2/3 binding regions were more often present near the transcription start sites. Motif analysis also revealed that activator protein 1 (AP‐1) sites were especially enriched in the sites common to Smad2/3 and Smad4 binding regions. In contrast, GC‐rich motifs were enriched in Smad4‐dominant binding regions. We further determined putative target genes of Smad4 whose expression was regulated by TGF‐β. Our findings revealed some general characteristics of Smad4 binding regions, and provide resources for examining the role of Smad4 in epithelial cells and cancer pathogenesis. ( Cancer Sci 2009)