Transcriptional profiling of the chick pineal gland, a photoreceptive circadian oscillator and pacemaker.

The avian pineal gland contains both circadian oscillators and photoreceptors to produce rhythms in biosynthesis of the hormone melatonin in vivo and in vitro. The molecular mechanisms for melatonin biosynthesis are largely understood, but the mechanisms driving the rhythm itself or the photoreceptive processes that entrain the rhythm are unknown. We have produced cDNA microarrays of pineal gland transcripts under light-dark and constant darkness conditions. Rhythmic transcripts were classified according to function, representing diverse functional groups, including phototransduction pathways, transcription/translation factors, ion channel proteins, cell signaling molecules, and immune function genes. These were also organized relative to time of day mRNA abundance in light-dark and constant darkness. The transcriptional profile of the chick pineal gland reveals a more complex form of gene regulation than one might expect from a gland whose sole apparent function is the rhythmic biosynthesis of melatonin. The mRNAs encoding melatonin biosynthesis are rhythmic as are many orthologs of mammalian "clock genes." However, the oscillation of phototransductive, immune, stress response, hormone binding, and other important processes in the transcriptome of the pineal gland, raises new questions regarding the role of the pineal gland in circadian rhythm generation, organization, and avian physiology.

Transcriptional profiling of circadian patterns of mRNA expression in the chick retina.

Previous transcriptome analyses have identified candidate molecular components of the avian pineal clock, and herein we employ high density cDNA microarrays of pineal gland transcripts to determine oscillating transcripts in the chick retina under daily and constant darkness conditions. Subsequent comparative transcriptome analysis of the pineal and retinal oscillators distinguished several transcriptional similarities between the two as well as significant differences. Rhythmic retinal transcripts were classified according to functional categories including phototransductive elements, transcription/translation factors, carrier proteins, cell signaling molecules, and stress response genes. Candidate retinal clock transcripts were also organized relative to time of day mRNA abundance, revealing groups accumulating peak mRNA levels across the circadian day but primarily reaching peak values at subjective dawn or subjective dusk. Comparison of the chick retina transcriptome to the pineal transcriptome under constant conditions yields an interesting group of conserved genes. This group includes putative clock elements cry1 and per3 in addition to several previously unidentified and uninvestigated genes exhibiting profiles of mRNA abundance that varied markedly under daily and constant conditions. In contrast, many transcripts were differentially regulated, including those believed to be involved in both melatonin biosynthesis and circadian clock mechanisms. Our results indicate an intimate transcriptional relationship between the avian pineal and retina in addition to providing previously uncharacterized molecular elements that we hypothesize to be involved in circadian rhythm generation.