RNA: Masters of regulation

This story is part of our series, Sculptors of the cell: RNA research at Whitehead Institute. Click here to see all stories in this collection. 

RNA plays an important role in making protein from DNA, but our bodies contain many different types of RNAs that also do other things. Messenger RNA (mRNA) is the molecule that carries copies of genetic information from DNA in the nucleus out into the main body of the cell, where the information in the mRNA is used as a template to make a protein. Other RNAs influence this process by regulating gene activity—determining how much protein is made from a gene at a given time in a given cell. 

How genes are regulated is what gives cells their specific identities. All the cells in your body contain the same DNA, so the difference between a skin cell and a brain cell comes down to how that DNA is used—the timing of when each protein is made, how much of the protein is made, and for how long. Genes are not regulated as if by a simple on or off switch but rather like a volume knob, tunable from off to low to very high. Regulatory RNAs assist with this tuning to help create the variety of cell types and more optimal gene activity patterns in each cell type. Researchers at Whitehead Institute have made important discoveries that have uncovered the prevalence, characteristics, and functions of regulatory RNAs. Their work has transformed researchers’ understanding of gene regulation and revealed a complex, elegant system that tailors gene expression for each cell type and tissue.

Not just dead weight

The DNA sequences that encode most regulatory RNAs reside in what researchers once dismissed as genomic dead weight — the more than 97% of the human genome that is called noncoding DNA because it does not produce, or encode, mRNA templates for proteins. Instead of dead weight, however, more recent tools and methods have uncovered that within this noncoding DNA is a treasure trove of invaluable elements including sequences encoding regulatory RNAs, such as microRNAs that tune protein production.

Consisting of only 22 nucleotides—the building blocks of DNA and RNA—microRNAs may be small, but their effects are mighty, resonating throughout evolution and development in both plants and animals. Whitehead Institute Member David Bartel likens microRNAs to sculptors of the transcriptome, chiseling away at gene expression. The role of a microRNA can be so important that removing its activity in mouse studies can have dramatic effects, including death (typically before or soon after birth), epilepsy, deafness, infertility, and cancer.

To regulate gene activity, microRNAs pair with specific mRNA sequences, typically triggering the mRNA’s destruction. Bartel’s lab has long been at the forefront of the microRNA field: He was the first to identify microRNAs in plants and one of three labs to first recognize the abundance of microRNAs in animals. Research from Bartel and others has shown that microRNAs regulate the production of most human proteins, meaning that the Bartel lab’s work uncovering the mechanisms underlying RNA regulation has implications for many aspects of human health and disease.

On target

Figuring out whether a particular microRNA is important in a certain biological process or disease of interest can be a challenge — one microRNA can affect the expression of hundreds of genes, which can complicate researchers’ efforts to understand its role. In order to address this challenge, Bartel devised a method that can predict a microRNA’s targets. In order to pinpoint the mRNAs that are most influenced by each microRNA, Bartel used his methodology to create TargetScan, the main tool that scientists use to obtain predictions of microRNA targets in humans and other organisms commonly used in research. With the help of TargetScan, researchers are better able to determine a microRNA’s function and place it within the context of a broader network of gene control. Researchers from around the world now rely on TargetScan; the site and the research behind it have been cited more than 19,000 times in a wide variety of papers involving microRNAs.

Bartel’s lab recently came up with a way to improve the targeting prediction information that they provide on TargetScan. Led by former graduate students Sean McGeary and Kathy Lin, the researchers developed a way to predict how strongly individual microRNAs will bind to different mRNAs. Previously, researchers used average microRNA behavior to predict the success rate of a microRNA repressing an mRNA. The new work allowed Bartel’s lab to measure different behavior for different microRNAs. They hope their improved microRNA targeting prediction model will make TargetScan an even more potent resource for researchers around the globe. 

Learn more here.

A family matter

Regulatory RNAs play important roles not just in animals but also in plants. One challenge of breeding plants is that certain crosses—pairings of a maternal plant and paternal plant of different strains—will not have viable seeds. Recently, Whitehead Institute Member Mary Gehring and postdoctoral researcher Satyaki Rajavasireddy determined how a gene regulatory pathway involving RNA affects whether seeds are able to survive and reach maturity in certain crosses within the common model plant Arabidopsis thaliana. 

This pathway involves RNA molecules that can influence gene activity through what are called epigenetic modifications. What makes epigenetic modifications special in the world of gene regulation is that they are reversible marks that can be passed down alongside the DNA sequences. The epigenetic pathway that the researchers observed affecting seed viability is RNA-directed DNA methylation, in which small RNAs control the addition of chemical tags called methyl groups to DNA. These tags in turn modify gene expression, often silencing or inactivating genes. When Rajavasireddy disabled this pathway in the paternal plant, he found that this corrected the expression of a small set of important genes, and so in turn allowed certain maternal-paternal crosses that otherwise would not have been successful to produce viable seeds. 

Learn more here and here.
 

A matter of time

Much of the subtle variation in gene activity between different cells is determined by controlling the lifespan of mRNAs. The longer an mRNA sticks around, the more protein can be made from it, meaning the gene is more highly expressed. Research in David Bartel’s lab, led by graduate students Timothy Eisen, Stephen Eichhorn, and Alex Subtelny, took an unprecedentedly in-depth, systematic look at the dynamics of mRNA decay to better understand what determines how long different mRNAs stick around.

mRNAs have tails made up of a string of adenosine nucleotides (one of the building blocks of RNA) that keep the mRNA stable. When a tail is shortened, the remaining molecule becomes unstable and vulnerable to decay. Researchers knew that mRNA molecules with long tails tend to last longer, but they didn’t know the specific rates of tail shortening for more than a few mRNAs. To better understand how genes are regulated, Bartel’s lab set out to determine these and other rates that govern mRNA decay.

The researchers discovered that things were not so simple as longer tail equals longer life. Instead, they found that mRNA tails could shorten at vastly different rates, with up to a thousand-fold difference between them. Their work also revealed new insights into differences in how rapidly mRNAs decay once their tail lengths become short. In related research, the lab uncovered how microRNAs can speed up degradation of mRNAs with short tails--a facet of microRNA’s regulatory behavior that was not previously appreciated.

Learn more here.

Turning the tables

MicroRNAs help control the rate at which mRNAs are degraded, regulating the amount of protein made. But what controls the rate at which a microRNA is degraded? Researchers in David Bartel’s lab, led by graduate student Charlie Shi, uncovered how certain mRNAs can turn the tables on microRNAs and cause the microRNA to be degraded.

Usually, when a microRNA binds to an mRNA, it kickstarts the process of the mRNA being destroyed. However, when the microRNA binds to particular target sites on an mRNA or other RNA, this instead triggers the microRNA’s destruction. This process, called target-directed microRNA degradation (TDMD), was known to occur in a few instances. Shi found that it is much more common than was previously known. He also discovered that it unfolds in an unexpected way. 

A microRNA usually sits inside of a large protein called Argonaute that protects the microRNA from enzymes in the cell that would degrade it. TDMD was thought to work by getting one end of the microRNA to stick out of its protective protein shell, causing it to be vulnerable to degradation. What Shi found shows that instead, TDMD works by flagging Argonaute for destruction, so that the microRNA’s protein protector is completely eliminated. This leaves the microRNA totally exposed in the cell, where it is destroyed by enzymes.

Learn more here.

Looking forward

As Bartel, Gehring, and others at Whitehead Institute tease apart RNA-based mechanisms regulating gene expression, their work continues to transform our perceptions of RNA’s role in gene control. No longer relegated to acting as a template for translation, RNAs such as microRNA and small RNAs are now recognized for actively tailoring gene expression profiles for specific cells and tissues. By applying emerging RNA-centric tools and methods, Whitehead Institute scientists may identify as-yet undiscovered types of regulatory RNA, uncover new facets of microRNA biology, and increase our appreciation for this crucial molecule in what may be the golden age of RNA research.