Systems analysis of circadian time-dependent neuronal epidermal growth factor receptor signaling

Daniel E Zak^*¹^,2 , Haiping Hao^*¹ , Rajanikanth Vadigepalli¹ , Gregory M Miller¹^,2 , Babatunde A Ogunnaike² and James S Schwaber¹

¹Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Thomas Jefferson University, Locust St, Philadelphia, PA, USA 19107

²Department of Chemical Engineering, University of Delaware, Academy St, Newark, DE, USA 19716

author email corresponding author email* Contributed equally

Genome Biology 2006, 7:R48doi:10.1186/gb-2006-7-6-r48


Published:	19 June 2006

Subject areas: Neurobiology, Cell biology

Abstract

Background

Identifying the gene regulatory networks governing physiological signal integration remains an important challenge in circadian biology. Epidermal growth factor receptor (EGFR) has been implicated in circadian function and is expressed in the suprachiasmatic nuclei (SCN), the core circadian pacemaker. The transcription networks downstream of EGFR in the SCN are unknown but, by analogy to other SCN inputs, we expect the response to EGFR activation to depend on circadian timing.

Results

We have undertaken a systems-level analysis of EGFR circadian time-dependent signaling in the SCN. We collected gene-expression profiles to study how the SCN response to EGFR activation depends on circadian timing. Mixed-model analysis of variance (ANOVA) was employed to identify genes with circadian time-dependent EGFR regulation. The expression data were integrated with transcription-factor binding predictions through gene group enrichment analyses to generate robust hypotheses about transcription-factors responsible for the circadian phase-dependent EGFR responses.

Conclusion

The analysis results suggest that the transcriptional response to EGFR signaling in the SCN may be partly mediated by established transcription-factors regulated via EGFR transription-factors (AP1, Ets1, C/EBP), transcription-factors involved in circadian clock entrainment (CREB), and by core clock transcription-factors (Rorα). Quantitative real-time PCR measurements of several transcription-factor expression levels support a model in which circadian time-dependent EGFR responses are partly achieved by circadian regulation of upstream signaling components. Our study suggests an important role for EGFR signaling in SCN function and provides an example for gaining physiological insights through systems-level analysis.