Identification and characterization of CCAAT/Enhancer Binding proteindelta (C/EBPdelta) target genes in G0 growth arrested mammary epithelial cells.

BACKGROUND: CCAAT/Enhancer Binding Proteindelta (C/EBPdelta) is a member of the highly conserved C/EBP family of leucine zipper (bZIP) proteins. C/EBPdelta is highly expressed in G0 growth arrested mammary epithelial cells (MECs) and "loss of function" alterations in C/EBPdelta have been associated with impaired contact inhibition, increased genomic instability and increased cell migration. Reduced C/EBPdelta expression has also been reported in breast cancer and acute myeloid leukemia (AML). C/EBPdelta functions as a transcriptional activator, however, only a limited number of C/EBPdelta target genes have been reported. As a result, the role of C/EBPdelta in growth control and the potential mechanisms by which "loss of function" alterations in C/EBPdelta contribute to tumorigenesis are poorly understood. The goals of the present study were to identify C/EBPdelta target genes using Chromatin Immunoprecipitation coupled with a CpG Island (HCG12K) Array gene chip ("ChIP-chip") assay and to assess the expression and potential functional roles of C/EBPdelta target genes in growth control. RESULTS: ChIP-chip assays identified approximately 100 C/EBPdelta target gene loci which were classified by gene ontology (GO) into cell adhesion, cell cycle regulation, apoptosis, signal transduction, intermediary metabolism, gene transcription, DNA repair and solute transport categories. Conventional ChIP assays validated the ChIP-chip results and demonstrated that 14/14 C/EBPdelta target loci were bound by C/EBPdelta in G0 growth arrested MCF-12A MECs. Gene-specific RT-PCR analysis also demonstrated C/EBPdelta-inducible expression of 14/14 C/EBPdelta target genes in G0 growth arrested MCF-12A MECs. Finally, expression of endogenous C/EBPdelta and selected C/EBPdelta target genes was also demonstrated in contact-inhibited G0 growth arrested nontransformed human MCF-10A MECs and in mouse HC11 MECs. The results demonstrate consistent activation and downstream function of C/EBPdelta in growth arrested human and murine MECs. CONCLUSION: C/EBPdelta target genes were identified by a global gene array approach and classified into functional categories that are consistent with biological contexts in which C/EBPdelta is induced, such as contact-mediated G0 growth arrest, apoptosis, metabolism and inflammation. The identification and validation of C/EBPdelta target genes provides new insights into the mechanistic role of C/EBPdelta in mammary epithelial cell biology and sheds new light on the potential impact of "loss of function" alterations in C/EBPdelta in tumorigenesis.