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| Status |
Public on Sep 30, 2014 |
| Title |
A circadian gene expression atlas in mammals assayed by microarray |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
|
| Summary |
To characterize the role of the circadian clock in mouse physiology and behavior, we used RNA-seq and DNA arrays to quantify the transcriptomes of 12 mouse organs over time. We found 43% of all protein coding genes showed circadian rhythms in transcription somewhere in the body, largely in an organ-specific manner. In most organs, we noticed the expression of many oscillating genes peaked during transcriptional “rush hours” preceding dawn and dusk. Looking at the genomic landscape of rhythmic genes, we saw that they clustered together, were longer, and had more spliceforms than nonoscillating genes. Systems-level analysis revealed intricate rhythmic orchestration of gene pathways throughout the body. We also found oscillations in the expression of more than 1,000 known and novel noncoding RNAs (ncRNAs). Supporting their potential role in mediating clock function, ncRNAs conserved between mouse and human showed rhythmic expression in similar proportions as protein coding genes. Importantly, we also found that the majority of best-selling drugs and World Health Organization essential medicines directly target the products of rhythmic genes. Many of these drugs have short half-lives and may benefit from timed dosage. In sum, this study highlights critical, systemic, and surprising roles of the mammalian circadian clock and provides a blueprint for advancement in chronotherapy.
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| Overall design |
288 samples total covering 12 different tissues, with no replicates. Each tissue sampled every 2 hours for 2 days (24 samples per tissue).
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| Contributor(s) |
Zhang R, Lahens NF, Ballance HI, Hughes ME, Hogenesch JB |
| Citation(s) |
25349387 |
| Submission date |
Feb 04, 2014 |
| Last update date |
Mar 04, 2019 |
| Contact name |
Nicholas Lahens |
| Organization name |
University of Pennsylvania
|
| Department |
ITMAT
|
| Street address |
Smilow Center for Translational Research 10-110 3400 Civic Center Blvd, Bldg 421
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL6246 |
[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] |
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| Samples (288)
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| This SubSeries is part of SuperSeries: |
| GSE54652 |
A circadian gene expression atlas in mammals: Implications for biology and medicine |
|
| Relations |
| BioProject |
PRJNA237294 |
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