Posts tagged RNA molecules
Articles and news from the latest research reports.
Researchers obtain key insights into how the internal body clock is tuned
Researchers at UT Southwestern Medical Center have found a new way that internal body clocks are regulated by a type of molecule known as long non-coding RNA.
The internal body clocks, called circadian clocks, regulate the daily “rhythms” of many bodily functions, from waking and sleeping to body temperature and hunger. They are largely “tuned” to a 24-hour cycle that is influenced by external cues such as light and temperature.
“Although we know that long non-coding RNAs are abundant in many organisms, what they do in the body, and how they do it, has not been clear so far,” said Dr. Yi Liu, Professor of Physiology. “Our work establishes a role for long non-coding RNAs in ‘tuning’ the circadian clock, but also shows how they control gene expression.”
Determining how circadian clocks work is crucial to understanding several human diseases, including sleep disorders and depression in which the clock malfunctions. The influence of a functional clock is evident in the reduced performance of shift workers and the jet lag felt by long-distance travellers.
Dr. Liu and his team were able to learn more about the circadian rhythms by studying model systems involving the bread mold, Neurospora crassa. The researchers found that the expression of a clock gene named frequency (frq) is controlled by a long non-coding RNA named qrf (frq backwards) − an RNA molecule that is complementary, or antisense, to frq. Unlike normal RNA molecules, qrf does not encode a protein, but it can control whether and how much frq protein is produced.
Specifically, qrf RNA is produced in response to light, and can then interfere with the production of the frq protein. In this way, qrf can “re-set” the circadian clock in a light-dependent way. This regulation works both ways: frq can also block the production of qrf. This mutual inhibition ensures that the frq and qrf RNA molecules are present in opposite “phases” of the clock and allows each RNA to oscillate robustly. Without qrf, normal circadian rhythms are not sustained, indicating that the long non-coding RNA is required for clock functions.
The findings are published online in the journal Nature.
“We anticipate a similar mode of action may operate in other organisms because similar RNAs have been found for clock genes in mice. In addition, such RNAs may also function in other biological processes because of their wide presence in genomes,” said Dr. Liu, who is the Louise W. Kahn Scholar in Biomedical Research.
UT Southwestern investigators are leaders in unraveling the gene networks underlying circadian clocks and have shown that most body organs, such as the pancreas and liver, have their own internal clocks, and that virtually every cell in the human body contains a clock. It now appears that the clocks and clock-related genes – some 20 such genes have been identified – affect virtually all of the cells’ metabolic pathways, from blood sugar regulation to cholesterol production.
Other UT Southwestern researchers involved in the latest findings include Dr. Zhihong Xue, Qiaohong Ye, Dr. Juchen Yang and Dr. Guanghua Xiao. Support for this research included grants from the National Institutes of Health, the Welch Foundation, the Cancer Prevention Research Institute of Texas, and the Biotechnology and Biological Sciences Research Council.
“This study adds to an important body of work that has shown the ubiquity of a circadian clock across species, including humans, and its role in metabolic regulation in cells, organs, and organisms,” said Dr. Michael Sesma, Program Director in the Division of Genetics and Developmental Biology at the of the National Institutes of Health’s National Institute of General Medical Sciences, which partially funded the research. “These new results from Dr. Liu and his colleagues also extend beyond understanding the function of an anti-sense RNA in the fine tuning of a cell’s daily rhythm; they provide an example of the means by which anti-sense transcription likely regulates other key molecular and physiological processes in cells and organisms.”
(Image: Fotolia)
Researchers Discover How Brain Circuits Can Become Miswired During Development
Researchers at Weill Cornell Medical College have uncovered a mechanism that guides the exquisite wiring of neural circuits in a developing brain — gaining unprecedented insight into the faulty circuits that may lead to brain disorders ranging from autism to mental retardation.
In the journal Cell, the researchers describe, for the first time, that faulty wiring occurs when RNA molecules embedded in a growing axon are not degraded after they give instructions that help steer the nerve cell. So, for example, the signal that tells the axon to turn — which should disappear after the turn is made — remains active, interfering with new signals meant to guide the axon in other directions.
The scientists say that there may be a way to use this new knowledge to fix the circuits.
"Understanding the basis of brain miswiring can help scientists come up with new therapies and strategies to correct the problem," says the study’s senior author, Dr. Samie Jaffrey, a professor in the Department of Pharmacology.
"The brain is quite ‘plastic’ and changeable in the very young, and if we know why circuits are miswired, it may be possible to correct those pathways, allowing the brain to build new, functional wiring," he says.
Disorders associated with faulty neuronal circuits include epilepsy, autism, schizophrenia, mental retardation and spasticity and movement disorders, among others.
In their study, the scientists describe a process of brain wiring that is much more dynamic than was previously known — and thus more prone to error.
Proteins Sense the Environment to Steer the Axon
During brain development, neurons have to connect to each other, which they do by extending their long axons to touch one another. Ultimately, these neurons form a circuit between the brain and the target tissue through which chemical and electrical signals are relayed. In this study, researchers investigated neurons that travel up the spinal cord into the brain. “It is very critical that axons are precisely positioned in the spinal cord,” Dr. Jaffrey says. “If they are improperly positioned, they will form the wrong connections, which can lead to signals being sent to the wrong target cells in the brain.”
The way that an axon guides and finds its proper target is through so-called growth cones located at the tips of axons. “These growth cones have the ability to sense the environment, determine where the targets are and navigate toward them. The question has always been — how do they know how to do this? Where do the instructions come from that tell them how to find their proper target?” Dr. Jaffrey says. The team found that RNA molecules embedded in the growth cone are responsible for instructing the axon to move left or right, up or down. These RNAs are translated in growth cones to produce antenna-like proteins that steer the axon like a self-guided missile.
"As a circuit is being built, RNAs in the neuron’s growth cones are mostly silent. We found that specific RNAs are only read at precise stages in order to produce the right protein needed to steer the axon at the right time. After the protein is produced, we saw that the RNA instruction is degraded and disappears," he says.
"If these RNAs do not disappear when they should, the axon does not position itself properly — it may go right instead of left — and the wiring will be incorrect and the circuit may be faulty," Dr. Jaffrey says.
RNAs have Tremendous Power over Brain Development
The research finding answers a long-standing puzzle in the quest to understand brain wiring, says Dr. Dilek Colak, a postdoctoral associate in Dr. Jaffrey’s laboratory.
"There have been a series of discoveries over the last five years showing that proteins that control RNA degradation are very important for brain development and, when they are mutated, you can have spasticity or other movement disorders," Dr. Colak says. "That has raised a major question — why would RNA degradation pathways be so critical for properly creating brain circuits?
"What we show here is that not only does RNA need to be present in growth cones to give instructions, it then also needs to be removed from the growth cones to take away those instructions at the right time," she says. "Both those processes are critical and it may explain why there are so many different brain disorders associated with ineffective RNA regulation."
"The idea that control of brain wiring is located in these RNA molecules that are constantly being dynamically turned over is something that we didn’t anticipate," Dr. Jaffrey adds. "This tells us that regulating these RNA degradation pathways could have a tremendous impact on brain development. Now we know where to look to tease apart this process when it goes awry, and to think about how we can repair it."
(Image: Chad Baker)
Scientists Create Novel Approach to Find RNAs Involved in Long-term Memory Storage
Despite decades of research, relatively little is known about the identity of RNA molecules that are transported as part of the molecular process underpinning learning and memory.
Now, working together, scientists from the Florida campus of The Scripps Research Institute (TSRI), Columbia University and the University of Florida, Gainesville, have developed a novel strategy for isolating and characterizing a substantial number of RNAs transported from the cell-body of neuron (nerve cell) to the synapse, the small gap separating neurons that enables cell to cell communication.
Using this new method, the scientists were able to identify nearly 6,000 transcripts (RNA sequences) from the genome of Aplysia, a sea slug widely used in scientific investigation.
The scientists’ target is known as the synaptic transcriptome—roughly the complete set of RNA molecules transported from the neuronal cell body to the synapse.
In the study, published recently in the journal Proceedings of the National Academy of Sciences, the scientists focused on the RNA transport complexes that interact with the molecular motor kinesin; kinesin proteins move along filaments known as microtubules in the cell and carry various gene products during the early stage of memory storage.
While neurons use active transport mechanisms such as kinesin to deliver RNA cargos to synapses, once they arrive at their synaptic destination that service stops and is taken over by other, more localized mechanisms—in much the same way that a traveler’s bags gets handed off to the hotel doorman once the taxi has dropped them at the entrance.
The scientists identified thousands of these unique sequences of both coding and noncoding RNAs. As it turned out, several of these RNAs play key roles in the maintenance of synaptic function and growth.
The scientists also uncovered several antisense RNAs (paired duplicates that can inhibit gene expression), although what their function at the synapse might be remains unknown.
“Our analyses suggest that the transported RNAs are surprisingly diverse,” said Sathya Puthanveettil, a TSRI assistant professor who designed the study. “It also brings up an important question of why so many different RNAs are transported to synapses. One reason may be that they are stored there to be used later to help maintain long-term memories.”
The team’s new approach offers the advantage of avoiding the dissection of neuronal processes to identify synaptically localized RNAs by focusing on transport complexes instead, Puthanveettil said. This new approach should help in better understanding changes in localized RNAs and their role in local translation as molecular substrates, not only in memory storage, but also in a variety of other physiological conditions, including development.
“New protein synthesis is a prerequisite for maintaining long term memory,” he said, “but you don’t need this kind of transport forever, so it raises many questions that we want to answer. What molecules need to be synthesized to maintain memory? How long is this collection of RNAs stored? What localized mechanisms come into play for memory maintenance? ”
(Source: scripps.edu)