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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

Restricted feeding changes the periodicity of 12 h rhythms.Mice were held in a restricted feeding paradigm (see Methods) and liver samples were collected every 2 h. Quantitative PCR was used to assess the transcriptional profile of eight genes: Hspa5 (A), Gmppb (B), Sec23b (C), Hspa1b (D), as well as Gramd3, Creld2, Gosr2 and Ints2 (data not shown). When compared to samples from ad libitum fed mice (red traces, right axis), restricted feeding samples (blue traces, left axis) showed only a single peak of expression over the course of a complete day (Error bars are +/−S.E.M.).
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pgen-1000442-g007: Restricted feeding changes the periodicity of 12 h rhythms.Mice were held in a restricted feeding paradigm (see Methods) and liver samples were collected every 2 h. Quantitative PCR was used to assess the transcriptional profile of eight genes: Hspa5 (A), Gmppb (B), Sec23b (C), Hspa1b (D), as well as Gramd3, Creld2, Gosr2 and Ints2 (data not shown). When compared to samples from ad libitum fed mice (red traces, right axis), restricted feeding samples (blue traces, left axis) showed only a single peak of expression over the course of a complete day (Error bars are +/−S.E.M.).

Mentions: Food metabolism represents a candidate driver of these cues. To address this, we examined 12 h transcripts in a restricted feeding paradigm. Under normal circumstances, mice feed almost exclusively during the night and generally have a larger meal shortly after lights out [31]. In this restricted feeding design, the availability of food is restricted to an 8 h time window during the subjective day, when mice are normally asleep and not eating. Previous experiments have shown that core clock components in the liver invert their phase by 12 h during restricted feeding [32]. We tested the expression pattern of 12 h genes using quantitative PCR and found that seven of the eight genes dramatically changed their expression patterns in response to restricted feeding, while one transcript became entirely arrhythmic (Figure 7 and data not shown). These genes maintained peak expression at approximately CT26, coinciding with feeding; however, the subjective evening peak was largely absent. Taken as a whole, these data support the hypothesis that at least one component of 12 h rhythms are driven by feeding.


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)

Restricted feeding changes the periodicity of 12 h rhythms.Mice were held in a restricted feeding paradigm (see Methods) and liver samples were collected every 2 h. Quantitative PCR was used to assess the transcriptional profile of eight genes: Hspa5 (A), Gmppb (B), Sec23b (C), Hspa1b (D), as well as Gramd3, Creld2, Gosr2 and Ints2 (data not shown). When compared to samples from ad libitum fed mice (red traces, right axis), restricted feeding samples (blue traces, left axis) showed only a single peak of expression over the course of a complete day (Error bars are +/−S.E.M.).
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1000442-g007: Restricted feeding changes the periodicity of 12 h rhythms.Mice were held in a restricted feeding paradigm (see Methods) and liver samples were collected every 2 h. Quantitative PCR was used to assess the transcriptional profile of eight genes: Hspa5 (A), Gmppb (B), Sec23b (C), Hspa1b (D), as well as Gramd3, Creld2, Gosr2 and Ints2 (data not shown). When compared to samples from ad libitum fed mice (red traces, right axis), restricted feeding samples (blue traces, left axis) showed only a single peak of expression over the course of a complete day (Error bars are +/−S.E.M.).
Mentions: Food metabolism represents a candidate driver of these cues. To address this, we examined 12 h transcripts in a restricted feeding paradigm. Under normal circumstances, mice feed almost exclusively during the night and generally have a larger meal shortly after lights out [31]. In this restricted feeding design, the availability of food is restricted to an 8 h time window during the subjective day, when mice are normally asleep and not eating. Previous experiments have shown that core clock components in the liver invert their phase by 12 h during restricted feeding [32]. We tested the expression pattern of 12 h genes using quantitative PCR and found that seven of the eight genes dramatically changed their expression patterns in response to restricted feeding, while one transcript became entirely arrhythmic (Figure 7 and data not shown). These genes maintained peak expression at approximately CT26, coinciding with feeding; however, the subjective evening peak was largely absent. Taken as a whole, these data support the hypothesis that at least one component of 12 h rhythms are driven by feeding.

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