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Circadian Rhythms and Gene Regulation02:19

Circadian Rhythms and Gene Regulation

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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...
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DNA Microarrays02:34

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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Related Experiment Video

Updated: Apr 30, 2026

Profiling of Pre-micro RNAs and microRNAs using Quantitative Real-time PCR qPCR Arrays
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Profiling of Pre-micro RNAs and microRNAs using Quantitative Real-time PCR qPCR Arrays

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Global profiling of the circadian transcriptome using microarrays.

Polly Yingshan Hsu1, Stacey L Harmer

  • 1Department of Plant Biology, University of California, Davis, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|May 6, 2014
PubMed
Summary

This study outlines a method for identifying circadian-regulated transcripts using microarrays and the JTK_CYCLE algorithm. It details experimental design and data analysis for understanding biological rhythms in Arabidopsis.

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Area of Science:

  • Molecular Biology
  • Chronobiology
  • Genomics

Background:

  • Circadian rhythms are endogenous 24-hour biological cycles.
  • High-throughput transcriptome analysis reveals widespread clock regulation in organisms.
  • Microarray experiments are crucial for studying gene expression over time.

Purpose of the Study:

  • To describe a comprehensive experimental and statistical procedure for identifying circadian-regulated transcripts.
  • To provide a detailed protocol for Arabidopsis using ATH1 microarrays and JTK_CYCLE.
  • To enable adaptation of the method for other organisms and expression platforms.

Main Methods:

  • Designing circadian time course microarray experiments.
  • RNA processing and gene expression profiling using ATH1 microarrays.
  • Statistical analysis with the JTK_CYCLE algorithm to identify rhythmic transcripts.

Main Results:

  • The study provides a validated methodology for circadian transcript discovery.
  • The described procedure effectively identifies clock-regulated genes in Arabidopsis.
  • The protocol is adaptable for various biological systems and transcriptomic platforms.

Conclusions:

  • The described method offers a robust approach to studying circadian transcriptomes.
  • This work facilitates the investigation of biological rhythms in diverse organisms.
  • The JTK_CYCLE algorithm combined with microarray data is effective for identifying rhythmic gene expression.