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J. Biol. Chem., Vol. 279, Issue 50, 52247-52254, December 10, 2004

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Transcriptional Profiling of Circadian Patterns of mRNA Expression in the Chick Retina^*

Michael J. Bailey, Phillip D. Beremand¶, Rick Hammer¶, Elizabeth Reidel¶, Terry L. Thomas¶, and Vincent M. Cassone||

From the Center for Biological Clocks Research, Department of Biology, and ^¶Laboratory for Functional Genomics, Texas A&M University, College Station, Texas 77843-3258

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.

Received for publication, May 21, 2004 , and in revised form, August 4, 2004.

^* This work supported by National Institutes of Health Grant PO1 NS39546. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains Tables 1–4.

^|| To whom correspondence and reprint requests should be addressed. Tel.: 979-845-2301; E-mail: vmc{at}mail.bio.tamu.edu.

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