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Related Experiment Video

Updated: May 10, 2026

Detection of RNA-binding Proteins by In Vitro RNA Pull-down in Adipocyte Culture

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Published on: July 22, 2016

Cold-induced RNA-binding proteins regulate circadian gene expression by controlling alternative polyadenylation.

Yuting Liu¹, Wenchao Hu, Yasuhiro Murakawa

¹CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.

Scientific Reports

|June 25, 2013

Summary

Two cold-induced RNA-binding proteins, Cirbp and Rbm3, control circadian gene expression by regulating alternative polyadenylation. Their depletion disrupts circadian rhythms by altering 3'UTR length and polyadenylation site selection.

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Area of Science:

Chronobiology
Molecular Biology
Gene Regulation

Background:

Body temperature synchronizes mammalian circadian rhythms via unknown mechanisms.
Circadian gene expression is crucial for physiological processes.
RNA-binding proteins (RBPs) play roles in post-transcriptional regulation.

Purpose of the Study:

To investigate the role of cold-induced RBPs, Cirbp and Rbm3, in temperature-entrained circadian gene expression.
To elucidate the mechanism by which these RBPs regulate circadian rhythms.

Main Methods:

Depletion of Cirbp and Rbm3 in mammalian cells.
Poly(A)-tail-specific RNA immunoprecipitation followed by sequencing (PAR-CLIP) to identify RBP binding sites.
Analysis of 3'UTR length and polyadenylation site (PAS) usage.
Measurement of core circadian gene expression amplitudes.

Main Results:

Depletion of Cirbp or Rbm3 significantly reduced the amplitude of core circadian genes.
Cirbp and Rbm3 bind to 3'UTRs near polyadenylation sites.
Cirbp/Rbm3 depletion shortened 3'UTRs; low temperature (upregulating Cirbp/Rbm3) lengthened them.
Cirbp and Rbm3 repress proximal PAS usage, influencing circadian oscillations in PAS selection.

Conclusions:

Cirbp and Rbm3 are key regulators of temperature-entrained circadian gene expression.
These RBPs control circadian rhythms by modulating alternative polyadenylation (APA).
APA is a critical mechanism for synchronizing peripheral clocks to body temperature cues.