Orthogonal analysis of C/EBPβ targets in vivo during liver proliferation

doi:10.1073/pnas.0402875101

Orthogonal analysis of C/EBPβ targets in vivo during liver proliferation

Departments of ^*Genetics, ^†Pediatrics, and ^§Medicine, ^¶Center for Bioinformatics, and ^∥Genomics Institute, Bioinformatics Core, University of Pennsylvania School of Medicine, Philadelphia, PA 19104

Edited by Peter K. Vogt, The Scripps Research Institute, La Jolla, CA, and approved July 27, 2004 (received for review April 23, 2004)

Abstract

CCAAT enhancer-binding protein β (C/EBPβ), a basic-leucine zipper transcription factor, is an important effector of signals in physiologic growth and cancer. The identification of direct C/EBPβ targets in vivo has been limited by functional compensation by other C/EBP family proteins and the low stringency of the consensus sequence. Here we use the combined power of expression profiling and high-throughput chromatin immunoprecipitation to identify direct and biologically relevant targets of C/EBPβ. We identified 25 potential C/EBPβ targets, of which 88% of those tested were confirmed as in vivo C/EBPβ-binding sites. Six of these genes also displayed differential expression in C/EBPβ^–/– livers. Computational analysis revealed that bona fide C/EBPβ target genes can be distinguished by the presence of binding motifs for specific additional transcription factors in the vicinity of the C/EBPβ site. This approach is generally applicable to the discovery of direct, biologically relevant targets of mammalian transcription factors.

Footnotes

↵ ** To whom correspondence should be addressed. E-mail: greenbal{at}mail.med.upenn.edu.
↵ ‡ J.R.F. and B.L. contributed equally to this work.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations: C/EBP, CCAAT enhancer-binding protein; ChIP, chromatin immunoprecipitation; PSSM, position-sensitive scoring matrices; ROC, receiver operating characteristics; PEPCK, phosphoenolpyruvate carboxykinase; PPAR, peroxisome proliferator-activated receptor.