Research article

Proximal genomic localization of STAT1 binding and regulated transcriptional activity

Samuel Wormald¹ , Douglas J Hilton² , Gordon K Smyth¹ and Terence P Speed^1,3

¹Division of Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia

²Division of Molecular Medicine, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia

³Department of Statistics, University of California, Berkeley, California, USA

author email corresponding author email

BMC Genomics 2006, 7:254doi:10.1186/1471-2164-7-254

Published:	11 October 2006

Abstract

Background

Signal transducer and activator of transcription (STAT) proteins are key regulators of gene expression in response to the interferon (IFN) family of anti-viral and anti-microbial cytokines. We have examined the genomic relationship between STAT1 binding and regulated transcription using multiple tiling microarray and chromatin immunoprecipitation microarray (ChIP-chip) experiments from public repositories.

Results

In response to IFN-γ, STAT1 bound proximally to regions of the genome that exhibit regulated transcriptional activity. This finding was consistent between different tiling microarray platforms, and between different measures of transcriptional activity, including differential binding of RNA polymerase II, and differential mRNA transcription. Re-analysis of tiling microarray data from a recent study of IFN-γ-induced STAT1 ChIP-chip and mRNA expression revealed that STAT1 binding is tightly associated with localized mRNA transcription in response to IFN-γ. Close relationships were also apparent between STAT1 binding, STAT2 binding, and mRNA transcription in response to IFN-α. Furthermore, we found that sites of STAT1 binding within the Encyclopedia of DNA Elements (ENCODE) region are precisely correlated with sites of either enhanced or diminished binding by the RNA polymerase II complex.

Conclusion

Together, our results indicate that STAT1 binds proximally to regions of the genome that exhibit regulated transcriptional activity. This finding establishes a generalized basis for the positioning of STAT1 binding sites within the genome, and supports a role for STAT1 in the direct recruitment of the RNA polymerase II complex to the promoters of IFN-γ-responsive genes.