Corporate Banner
Satellite Banner
Technology
Networks
Scientific Communities
 
Become a Member | Sign in
Home>News>This Article
  News
Return

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

Join For Free

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 3,200+ scientific posters on ePosters
  • More Than 4,600+ 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 TechnologyNetworks.com 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
Platelets are the Pathfinders for Leukocyte Extravasation During Inflammation
Findings from the study could help in the prevention and treatment of inflammatory pathologies.
ASMS 2016: Targeting Mass Spectrometry Tools for the Masses
The expanding application range of MS in life sciences, food, energy, and health sciences research was highlighted at this year's ASMS meeting in San Antonio, Texas.
Benchtop Automation Trends
Gain a better understanding of current interest in and future deployment of benchtop automated systems.
Manufactured Stem Cells to Advance Clinical Research
Clinical-grade cell line will enable development of new therapies and accelerate early-stage clinical research.
Dengue Virus Exposure May Amplify Zika Infection
Researchers at Imperial College London have found that the previous exposure to the dengue virus may increase the potency of Zika infection.
Gender Determination in Forensic Investigations
This study investigated the effectiveness of lip print analysis as a tool in gender determination.
Identifying Novel Types of Forensic Markers in Degraded DNA
Scientists have tried to verify the nucleosome protection hypothesis by discovering STRs within nucleosome core regions, using whole genome sequencing.
Proteins in Blood of Heart Disease Patients May Predict Adverse Events
Nine-protein test shown superior to conventional assessments of risk.
Higher Frequency of Huntington's Disease Mutations Discovered
University of Aberdeen study shows that the gene change that causes Huntington's disease is much more common than previously thought.
Starving Stem Cells May Enable Scientists To Build Better Blood Vessels
Researchers from the University of Illinois at Chicago College of Medicine have uncovered how changes in metabolism of human embryonic stem cells help coax them to mature into specific cell types — and may improve their function in engineered organs or tissues.
Scroll Up
Scroll Down
Skyscraper Banner

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
3,200+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
4,600+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FOR FREE!