JunD/AP1 regulatory network analysis during macrophage activation in a rat model of crescentic glomerulonephritis

BackgroundFunction and efficiency of a transcription factor (TF) are often modulated by interactions with other proteins or TFs to achieve finely tuned regulation of target genes. However, complex TF interactions are often not taken into account to identify functionally active TF-targets and characterize their regulatory network. Here, we have developed a computational framework for integrated analysis of genome-wide ChIP-seq and gene expression data to identify the functional interacting partners of a TF and characterize the TF-driven regulatory network. We have applied this methodology in a rat model of macrophage dependent crescentic glomerulonephritis (Crgn) where we have previously identified JunD as a TF gene responsible for enhanced macrophage activation associated with susceptibility to Crgn in the Wistar-Kyoto (WKY) strain.ResultsTo evaluate the regulatory effects of JunD on its target genes, we analysed data from two rat strains (WKY and WKY.LCrgn2) that show 20-fold difference in their JunD expression in macrophages. We identified 36 TFs interacting with JunD/Jun and JunD/ATF complexes (i.e., AP1 complex), which resulted in strain-dependent gene expression regulation of 1,274 target genes in macrophages. After lipopolysaccharide (LPS) stimulation we found that 2.4 fold more JunD/ATF-target genes were up-regulated as compared with JunD/Jun-target genes. The enriched 314 genes up-regulated by AP1 complex during LPS stimulation were most significantly enriched for immune response (P = 6.9 × 10-4) and antigen processing and presentation functions (P = 2.4 × 10-5), suggesting a role for these genes in macrophage LPS-stimulated activation driven by JunD interaction with Jun/ATF.ConclusionsIn summary, our integrated analyses revealed a large network of TFs interacting with JunD and their regulated targets. Our data also suggest a previously unappreciated contribution of the ATF complex to JunD-mediated mechanisms of macrophage activation in a rat model of crescentic glomerulonephritis.

[1]  R. Myers,et al.  Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data , 2005, Nucleic acids research.

[2]  E. Petretto,et al.  Combined ChIP-Seq and transcriptome analysis identifies AP-1/JunD as a primary regulator of oxidative stress and IL-1β synthesis in macrophages , 2013, BMC Genomics.

[3]  Alexander E. Kel,et al.  TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..

[4]  Enrico Petretto,et al.  Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans , 2006, Nature.

[5]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[6]  R. Tibshirani,et al.  Significance analysis of microarrays applied to the ionizing radiation response , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Kathleen A. Kennedy,et al.  Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4 , 2006, Nature.

[8]  Terence P. Speed,et al.  A comparison of normalization methods for high density oligonucleotide array data based on variance and bias , 2003, Bioinform..

[9]  T. Borodina,et al.  The BTB and CNC Homology 1 (BACH1) Target Genes Are Involved in the Oxidative Stress Response and in Control of the Cell Cycle* , 2011, The Journal of Biological Chemistry.

[10]  Saurabh Sinha,et al.  Stubb: a program for discovery and analysis of cis-regulatory modules , 2006, Nucleic Acids Res..

[11]  Gary D. Stormo,et al.  The AP-1 transcription factor Batf controls TH17 differentiation , 2009, Nature.

[12]  G. Lyons,et al.  Characterization of murine BATF: a negative regulator of activator protein‐1 activity in the thymus , 2001, European journal of immunology.

[13]  Mike Tyers,et al.  BioGRID: a general repository for interaction datasets , 2005, Nucleic Acids Res..

[14]  Jianfei Hu,et al.  MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs , 2008, Nucleic acids research.

[15]  Tsonwin Hai,et al.  The molecular biology and nomenclature of the activating transcription factor/cAMP responsive element binding family of transcription factors: activating transcription factor proteins and homeostasis. , 2001, Gene.

[16]  Simon Tavaré,et al.  BayesPeak: Bayesian analysis of ChIP-seq data , 2009, BMC Bioinformatics.

[17]  Antti Honkela,et al.  Model-based method for transcription factor target identification with limited data , 2010, Proceedings of the National Academy of Sciences.

[18]  Eric P. Bishop,et al.  Expression profile analysis of the inflammatory response regulated by hepatocyte nuclear factor 4α , 2011, BMC Genomics.

[19]  P. Nelson,et al.  ATF and Jun transcription factors, acting through an Ets / CRE promoter module, mediate lipopolysaccharide inducibility of the chemokine RANTES in monocytic Mono Mac 6 cells , 2000, European journal of immunology.

[20]  Jared C. Roach,et al.  Transcription factor expression in lipopolysaccharide-activated peripheral-blood-derived mononuclear cells , 2007, Proceedings of the National Academy of Sciences.

[21]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Martin C. Frith,et al.  Inferring transcription factor complexes from ChIP-seq data , 2011, Nucleic acids research.

[23]  A. Hoffmann,et al.  A Unifying Model for the Selective Regulation of Inducible Transcription by CpG Islands and Nucleosome Remodeling , 2009, Cell.

[24]  W. John Wilbur,et al.  PIE the search: searching PubMed literature for protein interaction information , 2012, Bioinform..

[25]  C. Daub,et al.  BMC Systems Biology , 2007 .

[26]  M. Daly,et al.  PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes , 2003, Nature Genetics.

[27]  W. Wong,et al.  ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells , 2009, Proceedings of the National Academy of Sciences.

[28]  Alan Salama,et al.  Jund is a determinant of macrophage activation and is associated with glomerulonephritis susceptibility , 2008, Nature Genetics.

[29]  E. Zandi,et al.  AP-1 function and regulation. , 1997, Current opinion in cell biology.

[30]  Michael Q. Zhang,et al.  Identifying cooperativity among transcription factors controlling the cell cycle in yeast. , 2003, Nucleic acids research.