Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Decoding DNA’s annotations

23.01.2012
A chemical probe that can differentiate between chemical tags adorning DNA could provide insights into how nature switches genes on and off

In the currently hot research area known as ‘epigenetics’, researchers are discovering that offspring inherit much more from their parents than just their genes. Individuals also inherit detailed instructions on how to use the genetic sequence coded in their DNA via small chemical, or epigenetic, markers that decorate DNA strands.


Figure 1: The Sp1 peptide probe (left) binds a DNA strand (right) and reveals the presence of an epigenetic marker that is a methyl group (purple). Copyright : 2011 Akimitsu Okamoto

The markers can activate some genes and switch off others. Epigeneticists are racing to decode the roles of different markers; but, first, they must develop the ability to read them. A new chemical probe, developed by a research team led by Akimitsu Okamoto at the RIKEN Advanced Science Institute, Wako, is showing promise as an analytical tool to assist this quest1.

The team’s probe can differentiate between two epigenetic markers—methyl and hydroxymethyl markers—that differ by the presence of a single oxygen atom. Methyl groups, one of the first epigenetic markers discovered, are known to inactivate gene expression; ‘demethylation’, or removal of a methyl group from the DNA, allows gene expression to restart.

“We know the mechanism of DNA methylation, but nobody knows the mechanism of DNA demethylation,” Okamoto explains. One possibility is that the body converts the methyl marker into a hydroxymethyl group, as the first step in the process of removing it, in preparation to reactivate a gene. However, current tests cannot distinguish between the two epigenetic markers, preventing that theory from being tested.

The chemical probe developed by Okamoto and colleagues is based on a peptide called Sp1, which is known to bind to DNA. The researchers previously modified the structure of Sp1 so that it adheres strongly only to DNA strands incorporating a methyl marker (Fig. 1). They then showed that if the peptide binds to a DNA strand, it reveals the presence of the methyl group2.
In their latest study, the researchers showed that modified Sp1 will not bind to DNA when the methyl group is converted to a hydroxymethyl—thereby allowing them to tell the two groups apart. The extra oxygen atom in the hydroxymethyl group disrupts the interaction between the peptide and the DNA, so the two cease to adhere together.

Okamoto and his colleagues are now planning to modify the peptide to detect an even wider range of epigenetic markers, which will allow the study of their role in gene expression. “Our next step is to develop the methods for effective sequencing and detection of DNA containing cytosine, 5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine,” Okamoto says.

The corresponding author for this highlight is based at the Nucleic Acid Chemistry Laboratory, RIKEN Advanced Science Institute

gro-pr | Research asia research news
Further information:
http://www.riken.jp
http://www.researchsea.com

More articles from Life Sciences:

nachricht A Map of the Cell’s Power Station
18.08.2017 | Albert-Ludwigs-Universität Freiburg im Breisgau

nachricht On the way to developing a new active ingredient against chronic infections
18.08.2017 | Deutsches Zentrum für Infektionsforschung

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Fizzy soda water could be key to clean manufacture of flat wonder material: Graphene

Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.

As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...

Im Focus: Exotic quantum states made from light: Physicists create optical “wells” for a super-photon

Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.

Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...

Im Focus: Circular RNA linked to brain function

For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.

While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...

Im Focus: RAVAN CubeSat measures Earth's outgoing energy

An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.

The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...

Im Focus: Scientists shine new light on the “other high temperature superconductor”

A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.

Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Call for Papers – ICNFT 2018, 5th International Conference on New Forming Technology

16.08.2017 | Event News

Sustainability is the business model of tomorrow

04.08.2017 | Event News

Clash of Realities 2017: Registration now open. International Conference at TH Köln

26.07.2017 | Event News

 
Latest News

A Map of the Cell’s Power Station

18.08.2017 | Life Sciences

Engineering team images tiny quasicrystals as they form

18.08.2017 | Physics and Astronomy

Researchers printed graphene-like materials with inkjet

18.08.2017 | Materials Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>