Summary: Researchers reveal the role hundreds of miRNAs appear to play in modulating circadian rhythm.
Source: USC
If you’ve ever suffered from jet lag, you know how disrupting the circadian rhythm can sap energy and impair performance. Molecular circadian “clocks” operate in cells across the body and influence far more than sleep and wake cycles; they affect metabolism, cognitive function and disease susceptibility. For more than a decade, scientists have focused on the protein-coding clock genes that drive rhythmic gene expression. New research published in the Proceedings of the National Academy of Sciences identifies an additional, genome-wide regulatory layer—microRNAs (miRNAs)—that modulate the circadian system.
Clock genes have long been central to circadian biology: they encode proteins that form transcription–translation feedback loops, producing daily oscillations in gene expression that govern physiology and behavior. But this new study uncovers the widespread influence of non-coding RNAs—short nucleotide sequences called microRNAs—that regulate protein production by blocking messenger RNA. The findings reveal that miRNAs form a previously underappreciated layer of circadian regulation, with potential implications for diseases from Alzheimer’s to diabetes and asthma.
“We’ve seen how the function of these clock genes is important in many diseases,” said Steve Kay, Provost Professor of neurology, biomedical engineering and quantitative computational biology at the Keck School of Medicine of USC. “What we were largely blind to was a whole different network of non-coding microRNAs that is also important for circadian regulation.”
“Junk DNA” proves to be a valuable tool in circadian rhythms
Once dismissed as “junk DNA,” many non-coding sequences, including miRNAs, are now recognized as powerful regulators of gene expression. Prior studies hinted that some miRNAs influence circadian clocks, but identifying which of the nearly thousand miRNAs in the genome participate in clock regulation remained a major challenge.
To tackle this, Lili Zhou, a research associate in USC’s Department of Neurology, partnered with the Genomics Institute of the Novartis Research Foundation (GNF) in San Diego. The institute’s high-throughput robotic platform enabled a genome-wide screen: each of approximately 989 miRNAs was introduced individually into human U2OS cells engineered with a luciferase reporter that pulses on and off with the cell’s 24-hour clock. This cell-based, systematic approach allowed the team to measure how each miRNA altered circadian period and rhythm.
“The collaboration with GNF made it possible for us to conduct the first cell-based, genome-wide screen to pinpoint which miRNAs might modulate circadian rhythms,” said Zhou.
“Much to our surprise,” said Kay, “we discovered about 110 to 120 miRNAs that do this.”
Following the screen, the team validated key candidates. With assistance from Caitlyn Miller, a USC undergraduate in biochemistry, researchers used genetic knockout approaches in their luminescent cell line to confirm causality: removing specific miRNAs produced the opposite effect on circadian timing compared with adding them, reinforcing that these miRNAs directly influence clock dynamics.
Physiologic and behavioral impacts of miRNAs
The study then probed physiological and behavioral consequences in animals. Mice lacking a specific miRNA cluster—miR-183/96/182—showed altered wheel-running behavior in the dark phase compared with control animals, demonstrating an impact at the behavioral level. Tissue-level analyses revealed that inactivating this miRNA cluster affected circadian rhythms differently across brain, retina and lung, indicating that miRNA regulation of the clock is tissue specific.
Mapping miRNA effects in individual tissues could open targeted approaches to treat or prevent diseases linked to circadian disruption. “In the brain we’re interested in connecting the clock to diseases like Alzheimer’s; in the lung we’re interested in connecting the clock to diseases like asthma,” Kay said. “The next step is to model disease states in animals and cells and examine how these microRNAs function within those disease contexts.”
About the study
The study’s co-authors include Caitlyn Miller (Keck School of Medicine of USC), Loren J. Miraglia and Angelica Romero (Genomics Institute of the Novartis Research Foundation), and Ludovic S. Mure and Satchidananda Panda (Salk Institute for Biological Studies), alongside lead investigators Lili Zhou and Steve A. Kay.
Funding: This work was supported by National Institute of Diabetes and Digestive and Kidney Diseases Grant 5R01DK108087 to S.A.K.
About this genetics research news
Source: USC
Contact: Laura LeBlanc – USC
Image: The image is in the public domain
Original Research: Closed access. “A genome-wide microRNA screen identifies the microRNA-183/96/182 cluster as a modulator of circadian rhythms” by Lili Zhou, Caitlyn Miller, Loren J. Miraglia, Angelica Romero, Ludovic S. Mure, Satchidananda Panda, and Steve A. Kay. PNAS
Abstract
A genome-wide microRNA screen identifies the microRNA-183/96/182 cluster as a modulator of circadian rhythms
Circadian rhythm regulation has been studied extensively at the level of transcription–translation feedback loops involving protein-coding genes, while regulatory modules composed of noncoding RNAs are less well understood. Emerging evidence highlights microRNAs (miRNAs) as important contributors to the robustness of the circadian network. To identify miRNAs capable of modulating circadian rhythms, the authors performed a genome-wide screen using U2OS luciferase reporter cells. From a library of 989 miRNAs, 120 altered period length in a dose-dependent manner. The study validated the miR-183/96/182 cluster both in vitro and in vivo, showing that each member of this cluster can modulate circadian rhythms and that miR-96 directly targets the core clock gene PER2. Knockout of the miR-183/96/182 cluster in mice produced tissue-specific changes in circadian parameters and altered behavioral rhythms. This work identifies a substantial set of miRNAs as circadian modulators, provides a resource for further study of miRNA roles in the circadian network, and underscores miRNAs as a genome-wide regulatory layer of clock control.