Junk DNA Role in Regulating Circadian Rhythms

summary: Researchers reveal the role hundreds of miRNAs appear to play in modulating circadian rhythm.

Source: USC

If you’ve ever had a bad case of jet lag, you know how a disruption to your body’s circadian rhythm makes it difficult to function. Molecular circadian “clocks” exist in cells throughout the body, governing more than just sleep and wake cycles – they are crucial to many aspects of human health. For more than a decade researchers have been trying to figure out what makes them tick, in search of new insights into diseases like Alzheimer’s, cancer, and diabetes.

Until now, that research has focused on what is known as clock genes, which encode proteins that drive oscillating cycles of gene expression affecting physiology and behavior. But research just published in the Proceedings of the National Academy of Sciences reveals the discovery of a new cog in the circadian clock – a genome-wide regulatory layer made up of small chains of non-coding nucleotides known as micro RNAs (miRNAs).

“We’ve seen how the function of these clock genes are really important in many different diseases,” said Steve Kay, Provost Professor of neurology, biomedical engineering, and quantitative computational biology at the Keck School of Medicine of USC. “But what we were blind to was a whole different funky kind of genes network that also is important for circadian regulation and this is the whole crazy world of what we call non-coding microRNA.”

“Junk DNA” proves to be a valuable tool in circadian rhythms

Formerly thought to be “junk DNA,” miRNAs are now known to affect gene expression by preventing messenger RNA from making proteins. Past research has indicated miRNAs may have a role in the function of circadian clocks but determining which of the hundreds of miRNAs in the genome might be involved remained a problem.

Kay and his team, led by Lili Zhou, a research associate in the Keck School’s Department of Neurology, turned to the Genomics Institute of the Novartis Research Foundation (GNF) in San Diego which has created robots capable of high throughput experiments. Working with scientists at the institute, Zhou developed a high throughput screen for a robot to test the close to 1000 miRNAs by individually transferring them into cells the team had engineered to glow on and off, based on the cell’s 24-hour circadian clock cycle.

“The collaboration with GNF made it possible for us to conduct the first cell-based, genome-wide screening approach to systematically identify which of the hundreds of miRNAs might be the ones modulating circadian rhythms,” said Zhou.

“Much to our surprise,” said Kay, “we discovered about 110 to 120 miRNAs that do this.”

With the help of Caitlyn Miller, a biochemistry undergraduate from USC Dornsife, researchers then verified the impact on circadian rhythms by inactivating certain miRNAs identified by the screen in their line of glowing cells. Knocking out the miRNAs had the opposite effect on the cells’ circadian rhythm as adding them to the cells.

Physiologic and behavioral impacts of miRNAs

Junk, DNA, Circadian, Rhythms

Researchers also focused on the physiologic and behavioral impacts of miRNAs. They analyzed the behavior of mice with a particular cluster of miRNAs inactivated – miR 183/96/182 – and saw that inactivating the cluster interfered with their wheel-running behavior in the dark compared with control mice. They then examined the impact of the miRNA cluster on the brain, retina, and lung tissue, and found that inactivating the cluster affected circadian rhythms differently in each tissue type – suggesting that the way the miRNAs regulate the circadian clock is tissue specific.

Understanding the impact of miRNAs on the circadian clock in individual tissue could reveal new ways of treating or preventing specific diseases.

“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,” said Kay. “The next step I think for us to model disease states in animals and cells and look at how these microRNAs are functioning in those disease states.”

About the study

Junk, DNA, Circadian, Rhythms

 

The study’s co-authors are Caitlyn Miller, Keck School of Medicine of USC, Loren J. Miraglia and Angelica Romero of the Genomics Institute of the Novartis Research Foundation, and Ludovic S. Mure and Satchidananda Panda of the Salk Institute for Biological Studies.

Funding: This work was supported by the 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

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Abstract

A genome-wide microRNA screen identifies the microRNA-183/96/182 cluster as a modulator of circadian rhythms

The regulatory mechanisms of circadian rhythms have been studied primarily at the level of the transcription-translation feedback loops of protein-coding genes. Regulatory modules involving noncoding RNAs are less thoroughly understood. In particular, emerging evidence has revealed the important role of microRNAs (miRNAs) in maintaining the robustness of the circadian system. To identify miRNAs that have the potential to modulate circadian rhythms, we conducted a genome-wide miRNA screen using U2OS luciferase reporter cells. Among 989 miRNAs in the library, 120 changed the period length in a dose-dependent manner. We further validated the circadian regulatory function of a miRNA cluster, miR-183/96/182, both in vitro and in vivo. We found that all three members of this miRNA cluster can modulate circadian rhythms. Particularly, miR-96 directly targeted a core circadian clock gene, PER2. The knockout of the miR-183/96/182 cluster in mice showed tissue-specific effects on circadian parameters and altered circadian rhythms at the behavioral level. This study identified a large number of miRNAs, including the miR-183/96/182 cluster, as circadian modulators. We provide a resource for further understanding of the role of miRNAs in the circadian network and highlight the importance of miRNAs as a genome-wide layer of circadian clock regulation.