Protein/DNA interaction profiling reveals novel regulators of the pineal transcriptome

The rat pineal gland transcriptome exhibits dynamic daily variation that reflects nocturnally restricted hormone production. Here we have used a protein/DNA interaction array to screen for day–night changes in DNA binding activity that are associated with transcriptional rhythms. Overall, 47 of 54 potential consensus binding sequence activities were detected, and of these, 29 (62%) were found to exhibit day:night differences in level. In addition to known, rhythmic pineal DNA binding activities (CRE and AP-1), multiple novel activities were observed including nocturnally elevated AP-2 consensus sequence binding activity. This array result was validated using conventional DNA binding assays, and we have also demonstrated AP-2β and AP-2γ proteins in the pineal gland, in addition to a nocturnally elevated AP-2α isoform. Our results have confirmed the presence of a complex assembly of transcriptional rhythms in the rat pineal gland and have provided details of more factors that contribute to this aspect of circadian neuroendocrine function.