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| Status |
Public on Jan 01, 2012 |
| Title |
Transcriptome in 129sv and Crx-/- pineal gland at ZT (Zeitgeber time) 6 and ZT20 |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
The cone-rod homeobox gene (Crx) encodes Crx, a transcription factor selectively expressed in two cell types, retinal photoreceptors and the melatonin secreting pinealocytes of the pineal gland. In this report the role of Crx in regulating gene expression in the mammalian pineal gland was extended using Affymetrix GeneChip technology. Deletion of Crx results in broad modulation of the mouse pineal transcriptome, including a >2-fold downregulation of 543 genes and a >2-fold upregulation of 745 genes. In addition to Crx, there was a >10-fold downregulation of 13 other genes. Of special interest was the discovery of a link between Crx and the homeobox gene Hoxc4, which was upregulated ~20-fold in the Crx-/- pineal gland. Analysis of night and day expression of genes indicated that a set of 51 genes exhibited differential expression in control animals.
Of these genes, only eight were also differentially expressed in Crx-/- animals. This group included Aanat, which encodes the enzyme that controls the daily rhythm in melatonin synthesis in the vertebrate pineal gland. Accordingly, Crx appears to be essential for the 24-hour rhythmic component of expression of some genes in the pineal gland. In the Crx-/- mouse pineal gland, 41 genes exhibited differential night/day expression that was not seen in control animals, suggesting that Crx may function to modulate rhythmic expression of these genes as well. Together, the results of this investigation indicate that Crx broadly modulates the pineal transcriptome, perhaps in part through suppressive effects on expression of the homeobox gene Hoxc4.
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| Overall design |
Pineal glands from control (129sv) mice and Crx-/- mice were collected at ZT6 and ZT20 for RNA extraction and hybridization on Affymetrix mouse 430_2 chip. Each condition were performed as triplicats.
SUPPLEMENTARY FILES:
The GCOS signal intensity data were analyzed using ChipInspector (Genomatix) version 2.1. FDR= 0, p-value <0.05, cut off=1, region size = 300 bp and 4 and 5 significant probes.
Log(2) fold change independently of time of day. Up regulated genes: genes which are up regulated in Crx-/- compared to the control; down regulated genes: genes which are down regulated in Crx-/- compared to the control.
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| Contributor(s) |
Rovsing L, Clokie S, Bustos DM, Rohde K, Coon S, Rath MF, Møller M, Klein DC |
| Citation(s) |
21797868 |
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| Submission date |
Oct 12, 2010 |
| Last update date |
Feb 11, 2019 |
| Contact name |
Louise Rovsing |
| E-mail(s) |
lrovsing@sund.ku.dk
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| Organization name |
Copenhagen University
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| Department |
Neuroscience and Pharmacology
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| Lab |
Circadian Group
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| Street address |
Blegdamsvej 3
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| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
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| Platforms (1) |
| GPL1261 |
[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array |
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| Samples (12)
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| GSM607394 |
Pineal gland from control mouse at ZT6, biological rep 1 |
| GSM607395 |
Pineal gland from control mouse at ZT6, biological rep 2 |
| GSM607396 |
Pineal gland from control mouse at ZT6, biological rep 3 |
| GSM607397 |
Pineal gland from control mouse at ZT20, biological rep 1 |
| GSM607398 |
Pineal gland from control mouse at ZT20, biological rep 2 |
| GSM607399 |
Pineal gland from control mouse at ZT20, biological rep 3 |
| GSM607400 |
Pineal gland from Crx-/- at ZT6, biological rep 1 |
| GSM607401 |
Pineal gland from Crx-/- at ZT6, biological rep 2 |
| GSM607402 |
Pineal gland from Crx-/- at ZT6, biological rep 3 |
| GSM607403 |
Pineal gland from Crx-/- at ZT20, biological rep 1 |
| GSM607404 |
Pineal gland from Crx-/- at ZT20, biological rep 2 |
| GSM607405 |
Pineal gland from Crx-/- at ZT20, biological rep 3 |
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| Relations |
| BioProject |
PRJNA132451 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE24625_RAW.tar |
48.2 Mb |
(http)(custom) |
TAR (of CEL) |
| GSE24625_down-genes_in_crx_vs_129.txt.gz |
8.8 Kb |
(ftp)(http) |
TXT |
| GSE24625_up-genes_in_crx_vs_129.txt.gz |
11.3 Kb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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