Identifying plant and animal DNA switches much faster and cheaper

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Identifying plant and animal DNA switches much faster and cheaper

PhD student devises new technique for ecological epigenetic research
Press release

It is not found in your genes but it ís hereditary. This defines epigenetic inheritance. The prefix 'epi' means 'upon' and here it is used to mean ‘on top of’ the DNA. Epigenetic changes to your DNA rapidly modify the activation and deactivation of genes and may determine a great deal.

‘It was simply impossible to dive in and make detailed assertions about epigenetic variations in a random plant species, without extensive prior knowledge,' explains NIOO researcher and creator of the new epiGBS technique, Thomas van Gurp. The correct tools were lacking. Together with lab technician Niels Wagemaker from Radboud University Nijmegen and researchers from Wageningen University, the epiGBS method was further developed and tested. ‘With our new method this is now possible.’


Smoking (gun)

Epigenetics has grown immensely as a field of research all across the world. In humans, for example, it has proved to be connected to the development of cancer cells and to environmental factors affecting the foetus during pregnancy. The latter include smoking and war-related distress.

Interest in epigenetics has also recently entered the field of ecological and evolutionary research. Are rapid epigenetic changes involved in surviving plagues and climate change?

The ability to adapt is vital in terms of ecology and evolution. Genetic adaptation takes time, but epigenetic changes can occur swiftly. ‘This is also of interest to growers of crops,’ explains Van Gurp. ‘Will it be possible to make the next generation of plants better adapted by giving the parent plants a specific treatment?’

What traits can a mother plant pass on to her children? Well, much more than just what's in her genes! Let's say you're a dandelion and hungry caterpillars are having their wicked way with you. Genetic adaptation takes much too much time to let you protect your 'children'. Fortunately the epigenetic route - what's on rather than in your genes - is much faster.

Epigenetic additions such as the methyl groups shown here as red dots can enable or disable specific genes. Need to taste bitter so that those nasty caterpillars will leave you alone? Epigenetics will switch on the right gene, making sure your children have a safe start in life. 'Thanks mum!'

How does it work?

How do you get started? First, you collect samples of dozens or even hundreds of plants. Then, you isolate the DNA. Now you apply the new method that only characterises certain pieces of the DNA for both the genes (genetic) as well as the modifications on the genes (epigenetic). Van Gurp continues to elaborate as he illustrates DNA strands with his arms, ‘This information can instantly reveal many things: that's that gene, that's that transposon, and this is epigenetic variation. This is a particularly useful method for (relatively) unstudied species, or what researchers call “without the reference genome of a model species".‘ And this can now all take place in the space of two weeks. This is particularly useful, because we only have a few model species versus an enormous biodiversity on our the planet.

Techniques for scanning for epigenetic methyl groups already exist. ‘But these techniques were either mostly incomplete or only possible if you already had a reference genome. In the first case you'd be left with a great amount of guesswork, while the second option was costly and time-consuming, meaning that it was never an option for normal species,’ explains senior researcher Koen Verhoeven. ‘We have now solved both of these problems.’ The researchers achieved this through a smart combination of DNA techniques and powerful bioinformatics, which put the pieces of information in the right place. ‘Starting with nothing, you are creating a genetic and epigenetic map for some thousands of pieces of DNA from your species of choice.’

This also immediately solves another significant issue: discrepancies in research results that sometimes occur between model species such as Arabidopsis, about which we know everything, and other species. ‘Is this the result of the differences between species or due to the utilisation of different techniques? That’s fatal for research!’ From now on, comparison is finally possible.'

Verhoeven continues, ‘This new technique has greatly furthered the field of ecological epigenetics.’

The NIOO counts more than 300 staff members and students and is one of the largest research institutes of the Royal Netherlands Academy of Arts and Sciences (KNAW). The institute specialises in water and land ecology. Since 2011, the institute is located in an innovative and sustainable research building located in Wageningen, the Netherlands. The institute has an impressive research history stretching back 60 years and which spans the entire country and beyond its borders..

For more information:

Article epiGBS: reference-free reduced representation bisulfite sequencing. Thomas P. van Gurp, Niels C.A.M. Wagemaker, Björn Wouters, Philippine Vergeer, Joop N.J. Ouborg & Koen J.F. Verhoeven. Nature Methods, the evening of 8 February 2016 (Advance Online Publication): www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3763.html