Nucleic Acids Research Advance Access published online on January 7, 2009
Nucleic Acids Research, doi:10.1093/nar/gkn1051
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Gene Regulation, Chromatin, and Epigenetics |
A ChIP–chip approach reveals a novel role for transcription factor IRF1 in the DNA damage response
1MRC Clinical Sciences Centre, Faculty of Medicine Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN and 2School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, NG7 2RD, UK
*To whom correspondence should be addressed. Tel: +44 115 951 5058; Fax: +44 115 846 8877; Email: nicole.clarke{at}nottingham.ac.uk
Received November 25, 2008. Accepted December 15, 2008.
IRF1 is a transcription factor that regulates key processes in the immune system and in tumour suppression. To gain further insight into IRF1's role in these processes, we searched for new target genes by performing chromatin immunoprecipitation coupled to a CpG island microarray (ChIP–chip). Using this approach we identified 202 new IRF1-binding sites with high confidence. Functional categorization of the target genes revealed a surprising cadre of new roles that can be linked to IRF1. One of the major functional categories was the DNA damage response pathway. In order to further validate our findings, we show that IRF1 can regulate the mRNA expression of a number of the DNA damage response genes in our list. In particular, we demonstrate that the mRNA and protein levels of the DNA repair protein BRIP1 [Fanconi anemia gene J (FANC J)] are upregulated after IRF1 over-expression. We also demonstrate that knockdown of IRF1 by siRNA results in loss of BRIP1 expression, abrogation of BRIP1 foci after DNA interstrand crosslink (ICL) damage and hypersensitivity to the DNA crosslinking agent, melphalan; a characteristic phenotype of FANC J cells. Taken together, our data provides a more complete understanding of the regulatory networks controlled by IRF1 and reveals a novel role for IRF1 in regulating the ICL DNA damage response.