Corporate Banner
Satellite Banner
Scientific Community
Become a Member | Sign in
Home>News>This Article

Some Long Non-Coding RNAs Are Conventional After All

Published: Monday, April 07, 2014
Last Updated: Monday, April 07, 2014
Bookmark and Share
Researchers have used ribosome profiling to identify several hundred long non-coding RNAs that may give rise to small peptides.

Not so long ago researchers thought that RNAs came in two types: coding RNAs that make proteins and non-coding RNAs that have structural roles. Then came the discovery of small RNAs that opened up whole new areas of research. Now researchers have come full circle and predicted that some long non-coding RNAs can give rise to small proteins that have biological functions. 

“We have identified hundreds of open reading frames in the long non-coding RNAs of humans and zebrafish that may give rise to functional proteins using ribosome profiling,” says Antonio Giraldez, one of the lead authors of the study and a professor at Yale University School of Medicine in the United States.

Ribosome profiling allows scientists to measure how much RNA is translated into protein. The method allows direct quantification of the messenger RNA fragments protected by the ribosome after digestion with the enzyme nuclease. The nucleases destroy the bonds between the exposed nucleotides that make up RNA and which are not protected by the protein-making machinery of the ribosome. What is left behind is a measurable amount of RNA destined to produce protein. 

The researchers were able to visualize translation and the movement of the ribosome every three nucleotides, which corresponds to the size of each codon on the RNA producing an amino acid. This was possible by combining the high resolution of ribosome profiling with a bioinformatic tool developed in the Giraldez laboratory called ORFScore.

“Crucial to our study was the parallel use of a second computational method that relies on a bioinformatic tool called micPDP,” says Giraldez. “micPDP revealed that the RNAs identified by ribosome profiling correspond to peptides that have been conserved over the course of evolution. This strongly suggests that these genes encode proteins that have specific functions in these animals.”

As a further validation of their method, the scientists went one step further and used mass spectrometry to detect and characterize almost 100 of the peptides coded by the RNAs.

Until recently, long non-coding RNAs were thought to be restricted to the more mundane but nonetheless important structural roles that are essential to support the function of the cell. “We think the main reason that these small functional peptides have been missed in earlier studies is due to the assumptions that have to be made when assigning functions to large numbers of genes,” says EMBO Member Nikolaus Rajewsky, Professor at the Max-Delbrück-Center in Berlin, Germany, Director of the Berlin Institute for Medical Systems Biology and one of the lead authors whose team contributed the micPDP computational method to identify conserved micropeptides. “Short open reading frames are so numerous that by design standard genome annotation methods have to filter out short open reading frames.”

There are many short peptides in nature, for example neuropeptides or insulin, but unlike the small peptides arising from long non-coding RNAs they are produced as larger preproteins that need to be trimmed to their final size. The first reports of activities for the small peptides produced by long non-coding RNAs have already begun to emerge. Schier and colleagues recently reported in Science1 a small peptide that functions as a signal to promote cell motility in the early fish embryo. The aptly named Toddler protein arises from long non-coding RNAs and acts as an activator of a G protein coupled receptor, one of the essential signaling molecules in the cell. Earlier work showed that a long non-coding RNA produced by the tarsal-less/polished rice/mille-pattes gene encodes small peptides that control epithelial morphogenesis in Drosophila and the flour beetle Tribolium.

“Our identification of hundreds of translated small open reading frames significantly expands the set of micropeptide-encoding vertebrate genes providing an entry point to investigate their real life functions,” says Giraldez.

“The peptide predictions reported in these studies are tantalizing, but this is just the first step. Things should get really interesting as the community explores the functions of the predicted peptides in vivo,” says Stephen M. Cohen, Professor at the Institute of Molecular and Cell Biology in Singapore who is not an author of the paper. “I imagine that we’ll be hearing a lot about this new peptide world in the years to come.”

Further Information
Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 2,800+ scientific posters on ePosters
  • More than 4,000+ scientific videos on LabTube
  • 35 community eNewsletters

Sign In

Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Scientific News
The Secret Behind the Power of Bacterial Sex
Migration between different communities of bacteria is the key to the type of gene transfer that can lead to the spread of traits such as antibiotic resistance, according to researchers at Oxford University.
Biomedical Imaging at One-Thousandth the Cost
Mathematical modeling enables $100 depth sensor to approximate the measurements of a $100,000 piece of lab equipment.
University of Glasgow Researchers Make An Impact in 60 Seconds
Early-career researchers were invited to submit an engaging, dynamic and compelling 60 second video illuminating an aspect of their research.
On Top of the Flu
Chance for advance warning in search-based tracking method.
TGAC Announces Milestone in Wheat Research
A more complete and accurate wheat genome assembly is being made available to researchers, by The Genome Analysis Centre (TGAC) on 12 November 2015.
Shedding Light on “Dark” Cellular Receptors
UNC and UCSF labs create a new research tool to find homes for two orphan cell-surface receptors, a crucial step toward finding better therapeutics and causes of drug side effects.
Is Allergy the Price We Pay for Our Immunity to Parasites?
New findings help demonstrate the evolutionary basis for allergy.
Questioning the Validity of Forensic DNA Match Statistic
Fifteen years of criminal cases with affected mixture evidence.
Predicting Adverse Drug Reactions with Higher Confidence
A new integrated computational method helps predicting adverse drug reaction—which are often lethal—more reliably than with traditional computing methods.
Healthcare and Life Sciences, Meet the Third Platform of Storage
Current EHR solutions are good for capturing and organizing patient information within a hospital environment, but they are not designed to organize data across the many systems.
Scroll Up
Scroll Down

Skyscraper Banner
Go to LabTube
Go to eposters
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
2,800+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
4,000+ scientific videos