Phenotyping Circadian Rhythms in Mice

Kristin Eckel‐Mahan1, Paolo Sassone‐Corsi2

1 University of Texas Health Sciences Center, Institute of Molecular Medicine, Houston, Texas, 2 University of California at Irvine, Department of Biological Chemistry, Center for Epigenetics and Metabolism, Irvine, California
Publication Name:  Current Protocols in Mouse Biology
Unit Number:   
DOI:  10.1002/9780470942390.mo140229
Online Posting Date:  September, 2015
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Circadian rhythms take place with a periodicity of 24 hr, temporally following the rotation of the earth around its axis. Examples of circadian rhythms are the sleep/wake cycle, feeding, and hormone secretion. Light powerfully entrains the mammalian clock and assists in keeping animals synchronized to the 24‐hour cycle of the earth by activating specific neurons in the “central pacemaker” of the brain, the suprachiasmatic nucleus. Absolute periodicity of an animal can deviate slightly from 24 hr as manifest when an animal is placed into constant dark or “free‐running” conditions. Simple measurements of an organism's activity in free‐running conditions reveal its intrinsic circadian period. Mice are a particularly useful model for studying circadian rhythmicity due to the ease of genetic manipulation, thus identifying molecular contributors to rhythmicity. Furthermore, their small size allows for monitoring locomotion or activity in their homecage environment with relative ease. Several tasks commonly used to analyze circadian periodicity and plasticity in mice are presented here including the process of entrainment, determination of tau (period length) in free‐running conditions, determination of circadian periodicity in response to light disruption (e.g., jet lag studies), and evaluation of clock plasticity in non‐24‐hour conditions (T‐cycles). Studying the properties of circadian periods such as their phase, amplitude, and length in response to photic perturbation, can be particularly useful in understanding how humans respond to jet lag, night shifts, rotating shifts, or other transient or chronic disruption of environmental surroundings. © 2015 by John Wiley & Sons, Inc.

Keywords: circadian; photic entrainment; tau; period; locomotion; phase; amplitude; light

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Table of Contents

  • Introduction
  • Basic Protocol 1: Circadian Phenotyping in Mice Entrainment and Determination of Period Length (TAU, ⊤) in Free‐Running Conditions
  • Alternate Protocol 1: Determination of the Range of Entrainment Using T Cycles
  • Support Protocol 1: Mimicking Jet Lag in Rodents
  • Commentary
  • Literature Cited
  • Figures
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Basic Protocol 1: Circadian Phenotyping in Mice Entrainment and Determination of Period Length (TAU, ⊤) in Free‐Running Conditions

  • Mice (control and experimental; a minimum of 6 per condition)
  • Enclosed room or light‐protected cages (insulation cabinets)
  • Standard mouse cages with bedding, food, water, and nestlets (refers to cages that are not light‐protected but rather housed in an enclosed room)
  • Cage body: 365 × 207 × 140, polycarbonate (Starr Life Sciences, cat. no. 1284L001), optional
  • Wire lid‐ steel inner lid with hinged divider (Starr Life Sciences, cat. no. 1284L116), optional
  • Infrared cage top motion detector (Starr Life Sciences, cat. no. 130‐0065‐AA or BIO‐LYNX in Canada, cat. no. 130‐0065‐AA) or running wheel, 4.5 diameter with reed switch (Starr Life Sciences, cat. no. 610‐0003‐00); wheel runners suitable for mice are also available at Columbus Instruments, cat. no. 0297‐0521 (
  • QA4 activity input modules (One module integrates 4 motion detectors or wheel runners; Starr Life Sciences, cat. no. 130‐0050‐00)
  • DP‐24 data port (Starr Life Sciences, cat. no. 840‐0024‐00 or BIO‐LYNX, cat. no. 840‐0024‐00); one DP24 integrates 24 sensors, 6 QA4 modules
  • C‐50 cable, 10 m (Starr Life Sciences, cat. no. 1076589 or BIO‐LYNX, cat. no. 060‐0045‐10)
  • Night vision goggles with infrared beam (can be acquired from a variety of stores); alternatively, dim red lighting can be used (see below)
  • Light timer (can be purchased from home improvement stores or may already be installed in an animal facility)
  • Lux meter (such as Cole‐Parmer Sper Scientific Light Meter, cat. no. UX‐50536‐05)
  • Opaque Tape and/or Black Plastic Sheeting to cover all light sources in the animal room (such as power lights on computers, activity monitors, etc.)
  • Computer Windows required for VitalView Software
  • VitalView Software with PCI Card (Starr Life Sciences, cat. no. 1098589 or BIO‐LYNX, cat. no. 855‐0035‐00): PC‐based data acquisition and analysis
  • ClockLabs (Coulbourn Instruments, ACT‐500) (required for the generation of single‐ and double‐plotted actograms, etc. from VitalView acquired data; requires MatLabs)
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Literature Cited

Literature Cited
  Aschoff, J. 1965. Response curves in circadian periodicity. Circadian Clocks 95‐111.
  Azzi, A., Dallmann, R., Casserly, A., Rehrauer, H., Patrignani, A., Maier, B., Kramer, A., and Brown, S.A. 2014. Circadian behavior is light‐reprogrammed by plastic DNA methylation. Nat. Neurosci. 17:377‐382. doi: 10.1038/nn.3651.
  Davidson, A.J., Sellix, M.T., Daniel, J., Yamazaki, S., Menaker, M., and Block, G.D. 2006. Chronic jet‐lag increases mortality in aged mice. Curr. Biol. 16:R914‐R916. doi: 10.1016/j.cub.2006.09.058.
  Gooley, J.J., Lu, J., Fischer, D., and Saper, C.B. 2003. A broad role for melanopsin in nonvisual photoreception. J. Neurosci. 23:7093‐7106.
  Jud, C., Schmutz, I., Hampp, G., Oster, H., and Albrecht, U. 2005. A guideline for analyzing circadian wheel‐running behavior in rodents under different lighting conditions. Biol. Proc. Online 7:101‐116. doi: 10.1251/bpo109.
  Refinetti, R. 2001. Dark adaptation in the circadian system of the mouse. Physiol. Behav. 74:101‐107. doi: 10.1016/S0031‐9384(01)00546‐7.
  Valentinuzzi, V.S., Scarbrough, K., Takahashi, J.S., and Turek, F.W. 1997. Effects of aging on the circadian rhythm of wheel‐running activity in C57BL/6 mice. Am. J. Physiol. 273:R1957‐R1964.
  Yamaguchi, Y., Suzuki, T., Mizoro, Y., Kori, H., Okada, K., Chen, Y., Fustin, J.M., Yamazaki, F., Mizuguchi, N., Zhang, J., Dong, X., Tsujimoto, G., Okuno, Y., Doi, M., and Okamura, H. 2013. Mice genetically deficient in vasopressin V1a and V1b receptors are resistant to jet lag. Science 342:85‐90. doi: 10.1126/science.1238599.
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