An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules.
BACKGROUND
The TGF-beta/SMAD pathway is part of a broader signaling network in which crosstalk between pathways occurs. While the molecular mechanisms of TGF-beta/SMAD signaling pathway have been studied in detail, the global networks downstream of SMAD remain largely unknown. The regulatory effect of SMAD complex likely depends on transcriptional modules, in which the SMAD binding elements and partner transcription factor binding sites (SMAD modules) are present in specific context.


RESULTS
To address this question and develop a computational model for SMAD modules, we simultaneously performed chromatin immunoprecipitation followed by microarray analysis (ChIP-chip) and mRNA expression profiling to identify TGF-beta/SMAD regulated and synchronously coexpressed gene sets in ovarian surface epithelium. Intersecting the ChIP-chip and gene expression data yielded 150 direct targets, of which 141 were grouped into 3 co-expressed gene sets (sustained up-regulated, transient up-regulated and down-regulated), based on their temporal changes in expression after TGF-beta activation. We developed a data-mining method driven by the Random Forest algorithm to model SMAD transcriptional modules in the target sequences. The predicted SMAD modules contain SMAD binding element and up to 2 of 7 other transcription factor binding sites (E2F, P53, LEF1, ELK1, COUPTF, PAX4 and DR1).


CONCLUSIONS
Together, the computational results further the understanding of the interactions between SMAD and other transcription factors at specific target promoters, and provide the basis for more targeted experimental verification of the co-regulatory modules.
Qin
Huaxia
H
Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA. huaxia.qin@gmail.com
Chan
Michael W Y
MW
Liyanarachchi
Sandya
S
Balch
Curtis
C
Potter
Dustin
D
Souriraj
Irene J
IJ
Cheng
Alfred S L
AS
Agosto-Perez
Francisco J
FJ
Nikonova
Elena V
EV
Yan
Pearlly S
PS
Lin
Huey-Jen
HJ
Nephew
Kenneth P
KP
Saltz
Joel H
JH
Showe
Louise C
LC
Huang
Tim H M
TH
Davuluri
Ramana V
RV
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D002843:Chromatin / Q000378:metabolism*; D020869:Gene Expression Profiling; D016678:Genome; D006801:Humans; D047468:Immunoprecipitation; D051379:Mice; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D051381:Rats; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D051785:Smad Proteins / Q000235:genetics / Q000378:metabolism*; D016212:Transforming Growth Factor beta / Q000235:genetics / Q000378:metabolism
D002843:Chromatin; D012333:RNA, Messenger; D051785:Smad Proteins; D016212:Transforming Growth Factor beta