E-GEOD-5292 - Circadian Transcriptome of the Chicken Pineal In Vitro

Status
Released on 4 July 2008, last updated on 27 March 2012
Organism
Gallus gallus
Samples (392)
Array (1)
Protocols (7)
Description
Chick pinealocytes exhibit all the characteristics of a complete circadian system, comprising photoreceptive inputs, molecular clockworks and an easily measured rhythmic output, melatonin biosynthesis. We used microarray analysis to investigate the expression of approximately 8000 genes within cultured pinealocytes subjected to both LD and DD cycles. We report that a reduced subset of genes were rhythmically expressed in vitro compared to those previously published in vivo, and that gene expression rhythms were lower in amplitude, although the functional distribution of the rhythmic transcriptome was largely similar. We also investigated the effects of 6-hour pulses of light or of norepinephrine on gene expression in free-running cultures during both subjective day and night. As expected, both light and norepinephrine inhibited melatonin production; however, the two treatments differentially up- or down-regulated specific sets of genes in a fashion that was dependent upon time of day. Our combined approach of utilizing a time of day study and a light/NE pulse microarray experiment allowed us to identify novel genes linking clock input to clock function within the pineal. We identified approximately 30 rhythmic, light-responsive, NE-insensitive genes with no previously known clock function, which may play a role in circadian regulation of the pineal. These are candidates for future functional genomics experiments to elucidate their potential role in pineal physiology. Keywords: circadian; avian; pineal; light; norepinephrine Microarray analysis was performed on pineal samples subjected to one of four experimental groups: cultures placed within a 12-hour light:12-hour dark cycle (LD); cultures placed in continuous darkness (DD); cultures subjected to a 6-hour light pulse beginning at either CT0 or CT12 (i.e., zero or 12 hours after the beginning of subjective day) or that received no light pulse; and cultures subjected to 6 hours of NE treatment beginning at either CT0 or CT12 or that received similarly administered vehicle. For LD and DD groups, time-course sampling was performed such that 6 samples were collected over the course of a day at 4-hour intervals. For the light pulse and NE administration groups, 2 samples were collected over the course of a day, either at CT6 or CT18 (i.e., 6 or 18 hours after the beginning of subjective day). Four biological replicates and two technical replicates (for each biological repeat) were performed for each sample. For the LD and DD groups, time-points ZT18 and CT18 served as the control reference for the time-course analysis. For the light pulse experiment, cultures that did not receive light served as the control. For the NE administration experiment, cultures that received vehicle served as the control. Dye swaps for performed for experimental samples from the light pulse and NE administration experiments.
Experiment type
transcription profiling by array 
Contacts
Phillip D. Beremand <beremand@mail.bio.tamu.edu>, Michael J Bailey, Phillip D Beremand, Stephen P Karaganis, Terry L Thomas, Vincent M Cassone, Vinod Kumar
Citation
Circadian genomics of the chick pineal gland in vitro. Karaganis SP, Kumar V, Beremand PD, Bailey MJ, Thomas TL, Cassone VM.
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-5292.idf.txt
Sample and data relationshipE-GEOD-5292.sdrf.txt
Processed data (1)E-GEOD-5292.processed.1.zip
Array designA-GEOD-3731.adf.txt
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