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Harmonics of circadian gene transcription in mammals.

Hughes ME, DiTacchio L, Hayes KR, Vollmers C, Pulivarthy S, Baggs JE, Panda S, Hogenesch JB - PLoS Genet. (2009)

Bottom Line: We recently developed a method to look at transcriptional oscillations with unprecedented precision and accuracy using high-density time sampling.Strikingly, we found two clusters of genes that cycle at the second and third harmonic of circadian rhythmicity in liver, but not cultured cells.Validation experiments show that 12-hour oscillatory transcripts occur in several other peripheral tissues as well including heart, kidney, and lungs.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmacology, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America.

ABSTRACT
The circadian clock is a molecular and cellular oscillator found in most mammalian tissues that regulates rhythmic physiology and behavior. Numerous investigations have addressed the contribution of circadian rhythmicity to cellular, organ, and organismal physiology. We recently developed a method to look at transcriptional oscillations with unprecedented precision and accuracy using high-density time sampling. Here, we report a comparison of oscillating transcription from mouse liver, NIH3T3, and U2OS cells. Several surprising observations resulted from this study, including a 100-fold difference in the number of cycling transcripts in autonomous cellular models of the oscillator versus tissues harvested from intact mice. Strikingly, we found two clusters of genes that cycle at the second and third harmonic of circadian rhythmicity in liver, but not cultured cells. Validation experiments show that 12-hour oscillatory transcripts occur in several other peripheral tissues as well including heart, kidney, and lungs. These harmonics are lost ex vivo, as well as under restricted feeding conditions. Taken in sum, these studies illustrate the importance of time sampling with respect to multiple testing, suggest caution in use of autonomous cellular models to study clock output, and demonstrate the existence of harmonics of circadian gene expression in the mouse.

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Related in: MedlinePlus

The peaks of 12 h cycling genes correlate with subjective dusk and dawn.Rhythmic transcripts detected by COSOPT and Fisher's G-test at a false-discovery rate of <0.05 were median-normalized and plotted as a heatmap for 24, 12 and 8 h cycling genes (A–C). Bright yellow represents expression 2-fold greater than median levels while bright blue represents expression less than 50 percent of median levels. The time of peak expression of 24 h cycling genes show a roughly equal distribution over the course of a day; in contrast, the peak expression of both 12 h rhythms are biased to specific times each day.
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pgen-1000442-g005: The peaks of 12 h cycling genes correlate with subjective dusk and dawn.Rhythmic transcripts detected by COSOPT and Fisher's G-test at a false-discovery rate of <0.05 were median-normalized and plotted as a heatmap for 24, 12 and 8 h cycling genes (A–C). Bright yellow represents expression 2-fold greater than median levels while bright blue represents expression less than 50 percent of median levels. The time of peak expression of 24 h cycling genes show a roughly equal distribution over the course of a day; in contrast, the peak expression of both 12 h rhythms are biased to specific times each day.

Mentions: In addition to improving the confidence by which both circadian and sub-circadian genes are identified, a 1 h sampling density increases the precision of phase estimates. At a 4 h resolution, only six different phases can be confidently assigned to circadian genes; in contrast, the current study allows the discrimination of phase differences of as little as 1 h. Consequently, subtle but nonetheless consistent phase differences have been identified between core components of the circadian clock (Figure S5). To extend this result, the expression of all cycling genes was median-normalized and plotted as a heat map (Figure 5). Conventional circadian genes show peak expression levels throughout the day with little bias in their phase (Figure 5A). In contrast, the majority of 12 h genes cluster into a single group with similar phases (Figure 5B). Interestingly, the peak of most 12 h genes coincides with dusk and dawn, suggesting that these genes may anticipate the stress of these daily transitions in light and darkness.


Harmonics of circadian gene transcription in mammals.

Hughes ME, DiTacchio L, Hayes KR, Vollmers C, Pulivarthy S, Baggs JE, Panda S, Hogenesch JB - PLoS Genet. (2009)

The peaks of 12 h cycling genes correlate with subjective dusk and dawn.Rhythmic transcripts detected by COSOPT and Fisher's G-test at a false-discovery rate of <0.05 were median-normalized and plotted as a heatmap for 24, 12 and 8 h cycling genes (A–C). Bright yellow represents expression 2-fold greater than median levels while bright blue represents expression less than 50 percent of median levels. The time of peak expression of 24 h cycling genes show a roughly equal distribution over the course of a day; in contrast, the peak expression of both 12 h rhythms are biased to specific times each day.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2654964&req=5

pgen-1000442-g005: The peaks of 12 h cycling genes correlate with subjective dusk and dawn.Rhythmic transcripts detected by COSOPT and Fisher's G-test at a false-discovery rate of <0.05 were median-normalized and plotted as a heatmap for 24, 12 and 8 h cycling genes (A–C). Bright yellow represents expression 2-fold greater than median levels while bright blue represents expression less than 50 percent of median levels. The time of peak expression of 24 h cycling genes show a roughly equal distribution over the course of a day; in contrast, the peak expression of both 12 h rhythms are biased to specific times each day.
Mentions: In addition to improving the confidence by which both circadian and sub-circadian genes are identified, a 1 h sampling density increases the precision of phase estimates. At a 4 h resolution, only six different phases can be confidently assigned to circadian genes; in contrast, the current study allows the discrimination of phase differences of as little as 1 h. Consequently, subtle but nonetheless consistent phase differences have been identified between core components of the circadian clock (Figure S5). To extend this result, the expression of all cycling genes was median-normalized and plotted as a heat map (Figure 5). Conventional circadian genes show peak expression levels throughout the day with little bias in their phase (Figure 5A). In contrast, the majority of 12 h genes cluster into a single group with similar phases (Figure 5B). Interestingly, the peak of most 12 h genes coincides with dusk and dawn, suggesting that these genes may anticipate the stress of these daily transitions in light and darkness.

Bottom Line: We recently developed a method to look at transcriptional oscillations with unprecedented precision and accuracy using high-density time sampling.Strikingly, we found two clusters of genes that cycle at the second and third harmonic of circadian rhythmicity in liver, but not cultured cells.Validation experiments show that 12-hour oscillatory transcripts occur in several other peripheral tissues as well including heart, kidney, and lungs.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmacology, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America.

ABSTRACT
The circadian clock is a molecular and cellular oscillator found in most mammalian tissues that regulates rhythmic physiology and behavior. Numerous investigations have addressed the contribution of circadian rhythmicity to cellular, organ, and organismal physiology. We recently developed a method to look at transcriptional oscillations with unprecedented precision and accuracy using high-density time sampling. Here, we report a comparison of oscillating transcription from mouse liver, NIH3T3, and U2OS cells. Several surprising observations resulted from this study, including a 100-fold difference in the number of cycling transcripts in autonomous cellular models of the oscillator versus tissues harvested from intact mice. Strikingly, we found two clusters of genes that cycle at the second and third harmonic of circadian rhythmicity in liver, but not cultured cells. Validation experiments show that 12-hour oscillatory transcripts occur in several other peripheral tissues as well including heart, kidney, and lungs. These harmonics are lost ex vivo, as well as under restricted feeding conditions. Taken in sum, these studies illustrate the importance of time sampling with respect to multiple testing, suggest caution in use of autonomous cellular models to study clock output, and demonstrate the existence of harmonics of circadian gene expression in the mouse.

Show MeSH
Related in: MedlinePlus