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Related Concept Videos

Circadian Rhythms and Gene Regulation02:19

Circadian Rhythms and Gene Regulation

The biological clock is involved in many aspects of regulating complex physiology in all animals. It was in 1935 when German zoologists, Hans Kalmus and Erwin Bünning, discovered the existence of circadian rhythm in Drosophila melanogaster. However, the internal molecular mechanisms behind the circadian clock remained a mystery until 1984, when Jeffrey C. Hall, Michael Rosbash, and Michael W. Young discovered the expression of the Per gene oscillating over a 24-hour cycle. In subsequent years,...
Circadian Rhythms and Gene Regulation02:19

Circadian Rhythms and Gene Regulation

The biological clock is involved in many aspects of regulating complex physiology in all animals. It was in 1935 when German zoologists, Hans Kalmus and Erwin Bünning, discovered the existence of circadian rhythm in Drosophila melanogaster. However, the internal molecular mechanisms behind the circadian clock remained a mystery until 1984, when Jeffrey C. Hall, Michael Rosbash, and Michael W. Young discovered the expression of the Per gene oscillating over a 24-hour cycle. In subsequent years,...
Biological Clocks and Seasonal Responses02:45

Biological Clocks and Seasonal Responses

The circadian—or biological—clock is an intrinsic, timekeeping, molecular mechanism that allows plants to coordinate physiological activities over 24-hour cycles called circadian rhythms. Photoperiodism is a collective term for the biological responses of plants to variations in the relative lengths of dark and light periods. The period of light-exposure is called the photoperiod.

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Rapid Analysis of Circadian Phenotypes in Arabidopsis Protoplasts Transfected with a Luminescent Clock Reporter
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Published on: September 17, 2016

Circadian phase has profound effects on differential expression analysis.

Polly Yingshan Hsu1, Stacey L Harmer

  • 1Department of Plant Biology, University of California Davis, Davis, California, United States of America.

Plos One
|November 28, 2012
PubMed
Summary

Circadian rhythms regulate gene expression. A mutation in Arabidopsis caused a phase shift, not altered gene levels, highlighting the clock's impact on transcriptomics and experimental design.

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Last Updated: May 16, 2026

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Published on: September 27, 2012

Area of Science:

  • Plant biology
  • Molecular biology
  • Genetics

Background:

  • Circadian rhythms are endogenous biological cycles crucial for organismal adaptation.
  • The circadian clock regulates a significant portion of gene expression across many species.
  • Previous studies often assume synchronized circadian phases when analyzing gene expression.

Purpose of the Study:

  • To investigate the impact of altered circadian phase on gene expression in Arabidopsis.
  • To determine if observed differential gene expression is due to phase shifts or actual expression level changes.
  • To provide a cautionary note on interpreting genome-wide expression data in the context of circadian rhythms.

Main Methods:

  • Analysis of a long-period mutant (rve8-1) in Arabidopsis under constant conditions.
  • Transcriptome-wide gene expression profiling using microarrays.
  • Differential gene expression analysis comparing mutant and wild-type plants.
  • Time-course sampling within a single genotype to assess phase effects.

Main Results:

  • The rve8-1 mutant exhibited a global phase alteration of clock-controlled genes.
  • Most differentially expressed genes in the mutant were attributed to phase differences, not expression level changes.
  • Even minor phase differences in wild-type plants significantly impacted differential expression analysis outcomes.

Conclusions:

  • The circadian clock profoundly influences transcriptome dynamics.
  • Phase differences are a critical factor to consider in gene expression studies.
  • Researchers must account for circadian phase to accurately interpret genome-wide expression data.