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

New RNA Sequencing technology helps reveal what plant genomes really encode

Published: Wednesday, July 25, 2012
Last Updated: Wednesday, July 25, 2012
Bookmark and Share
Scientists from the James Hutton Institute and the University of Dundee have teamed up with researchers in the USA to use a new technique to sequence the genes of the plant Arabidopsis. This approach, which allows researchers to see exactly where a plant's genes end, could be applied to crops in the hope of boosting efforts to breed new varieties.

 The Biotechnology and Biological Sciences Research Council (BBSRC)-funded team are the first in the world to try to understand how plant genes are organised by directly sequencing a molecule called RNA rather than DNA. Their findings are published today in the journal Nature Structural & Molecular Biology.

The research involved collaboration between a team of biologists led by Dr Gordon Simpson of The James Hutton Institute and Dundee University, computational scientists led by Prof Geoff Barton at Dundee University and a technology group from Helicos Biosciences in the USA.

Dr Simpson explains "Many genes work by coding for proteins, but the path from DNA to protein goes via an intermediate molecule called RNA. By sequencing the RNA you can see exactly which bits of the genome make proteins and what genes are turned on in different cells and at particular times.

"Until now, people have sequenced RNA by first converting it back into DNA. They chop it up, add on special molecules and then because there is not enough, they copy the bits again and again, before finally sequencing. The trouble is that all these steps introduce bias and error. What's special about what we have done is we have avoided all these steps and sequenced the RNA directly".

This technique allows scientists to see exactly where genes end with unprecedented certainty. This is important for two reasons. Firstly it helps us find individual genes within genomes and so work out what they do. Second, it tells us something about how cells are behaving. Cells can choose where a gene should end depending on what the gene should be doing. For example cutting off genes at different points affects when a plant flowers. It has recently become apparent that these choices occur widely in biology: for example, there are global changes in where genes end in cancer tissue.

Dr Simpson continues "Using this technique we can unequivocally score where genes end, count how active genes are and say from which strand of the DNA double helix the RNA is copied. Surprisingly we found that genes that overlap each other account for a large fraction of gene activity. We also found new ends to thousands of genes and found genes that were completely new to us".

The huge amount of data and the novelty of the procedure required new approaches from computational scientists in Dundee. Sasha Sherstnev, who did much of the analysis, comes from a background in particle physics and previously worked at CERN on the search for the Higgs Boson. He brought experience necessary to meet the demands accompanying the rise of large data sets in biology that are being driven by changes in sequencing technology.

As well as enabling scientists to understand what genomes actually encode and how active genes are, direct RNA sequencing could be especially useful for situations where only a few cells are available, for example when working with patient samples.

The Dundee team now plan to use their expertise to understand what other genomes encode and how that changes in disease. In this way, they can help deliver greater accuracy in rational crop improvement.

Professor Douglas Kell, Chief Executive, BBSRC, said "This is a great example of how mastering new techniques and embracing new ways of working can deliver valuable insights into biology. It will be interesting to see where this team directs their expertise next."


Notes to editors

This story is based on the paper "Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation" which can be found here on publication: Subscription may be required.


BBSRC invests in world-class bioscience research and training on behalf of the UK public. Our aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond.

Funded by Government, and with an annual budget of around £445M (2011-2012), we support research and training in universities and strategically funded institutes. BBSRC research and the people we fund are helping society to meet major challenges, including food security, green energy and healthier, longer lives. Our investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.

For more information about BBSRC, our science and our impact see:

For more information about BBSRC strategically funded institutes see:

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
Red Clover Genome to Help Restore Sustainable Farming
The Genome Analysis Centre (TGAC) in collaboration with IBERS, has sequenced and assembled the DNA of red clover to help breeders improve the beneficial traits of this important forage crop.
Turning up the Tap on Microbes Leads to Better Protein Patenting
Mining millions of proteins could become faster and easier with a new technique that may also transform the enzyme-catalyst industry, according to University of California, Davis, researchers.
Tardigrade's Are DNA Master Thieves
Tardigrades, nearly microscopic animals that can survive the harshest of environments, including outer space, hold the record for the animal that has the most foreign DNA.
GMO Food Animals Should be Judged by Product, Not Process
In a world with a burgeoning demand for meat, milk and eggs, regulatory policies around the use of biotechnologies in agriculture need to be based on the safety and attributes of those foods rather than on the methods used to produce them, says a UC Davis animal scientist.
Cancer-Fighting Tomato Component Traced
The metabolic pathway associated with lycopene, the bioactive red pigment found in tomatoes, has been traced by researchers at the University of Illinois.
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 the Origin of the Date Palm
Researchers also find ‘genetic mutation’ that is responsible for dates’ color.
New Way to Find DNA Damage
University of Utah chemists devised a new way to detect chemical damage to DNA that sometimes leads to genetic mutations responsible for many diseases, including various cancers and neurological disorders.
Speeding Up Potato Breeding
A joint project is investigating the potential of drones for speeding up the development of new potato varieties.
Gene Editing Could Enable Pig-To-Human Organ Transplant
The largest number of simultaneous gene edits ever accomplished in the genome could help bridge the gap between organ transplant scarcity and the countless patients who need them.
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
2,800+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
4,000+ scientific videos