Genome-Wide Analysis Reveals PADI4 Cooperates with Elk-1 to Activate c-Fos Expression in Breast Cancer Cells

Xuesen Zhang,Paul R Thompson,Corey P Causey,Matthew J Gamble,Mark S Roberson,Brian D Cherrington,Scott A Coonrod,W Lee Kraus,Sonja Stadler,Asifa Akhtar

doi:10.1371/journal.pgen.1002112

Xuesen Zhang, Paul R Thompson + Show 8 more

Open Access

https://doi.org/10.1371/journal.pgen.1002112

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Abstract

Peptidylarginine deiminase IV (PADI4) catalyzes the conversion of positively charged arginine and methylarginine residues to neutrally charged citrulline, and this activity has been linked to the repression of a limited number of target genes. To broaden our knowledge of the regulatory potential of PADI4, we utilized chromatin immunoprecipitation coupled with promoter tiling array (ChIP-chip) analysis to more comprehensively investigate the range of PADI4 target genes across the genome in MCF-7 breast cancer cells. Results showed that PADI4 is enriched in gene promoter regions near transcription start sites (TSSs); and, surprisingly, this pattern of binding is primarily associated with actively transcribed genes. Computational analysis found potential binding sites for Elk-1, a member of the ETS oncogene family, to be highly enriched around PADI4 binding sites; and coimmunoprecipitation analysis then confirmed that Elk-1 physically associates with PADI4. To better understand how PADI4 may facilitate gene transactivation, we then show that PADI4 interacts with Elk-1 at the c-Fos promoter and that, following Epidermal Growth Factor (EGF) stimulation, PADI4 catalytic activity facilitates Elk-1 phosphorylation, histone H4 acetylation, and c-Fos transcriptional activation. These results define a novel role for PADI4 as a transcription factor co-activator.

Highlights

The mitogen activated protein kinase/extracellular signalrelated kinase (MAPK/ERK) pathway couples extracellular signals with a range of intracellular responses including cell growth, proliferation, and differentiation
We looked across the human genome using Chromatin Immunoprecipitation (ChIP)-chip to better define the full repertoire of genes that are regulated by Peptidylarginine deiminase 4 (PADI4) in breast cancer cells
We found that PADI4 is likely recruited as a co-activator to these target genes by a range of well-defined transcription factors, such as Elk-1

Summary

Introduction

The mitogen activated protein kinase/extracellular signalrelated kinase (MAPK/ERK) pathway couples extracellular signals with a range of intracellular responses including cell growth, proliferation, and differentiation. The discovery that PADI4 is a nuclear enzyme which converts histone arginine residues to citrulline [15] provided the first evidence that PADI4 may play a role in gene regulation. This prediction was validated by the findings that PADI4 mediated citrullination of histone arginine residues (both unmodified and monomethylated) at the hormone dependent TFF1 promoter [16,17,18], and at the apoptosis related gene promoters, p21 and OKL38 [19,20], represses gene transcription.

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