Basic research has always had the tendency to contain surprising revelations on how the world functions. Whether in physics, chemistry, or biology. And in the case of biological studies, it is one of the reasons why model organisms are so important, as a reflection of all other organisms similar to them and as a way to go on a deep dive into the framework on how genetics and physiology combine to create life as we know it. If said research was spread generally across any and all organisms, that level of detail and understanding wouldn’t be possible. 

When it comes to the study of plants, the most widespread model organism is the thale cress, one of the few species that is more widely known by its taxonomic name of Arabidopsis thaliana than its common name. The major announcement of a new important discovery in plants that will change agriculture almost invariably results from an original study done using Arabidopsis. And it is yet another one of those very same studies that we’re discussing today.

Methylation Regulation

An important aspect to control over the genome of any organism is the regulatory systems that determine which genes are “turned on” and are being actively transcribed and translated into RNA and proteins and which ones are comparatively “off” in order to save on energy and to not introduce unneeded waste products. The way the individual genes are determined to be in either state is whether the DNA coding for them has been methylated or not. The addition of a methyl group of atoms to the DNA is a signal that that gene is not to be touched by the transcription hardware of our cells. But, if that’s how our genomes are set up to control what genes we need at any given time, then what systems actually cause methylation? And considering different parts of your body require different genes to be active, how do cells know what set of genes they need to be working with?

Researchers at the Salk Institute were asking these very questions when it came to plants, since we’ve known for a while that different parts from the leaves to the roots to the flowers all have different methylation patterns in their genomes. But how are these DNA controls regulated? What regulates the regulators? Over the past decade, some studies have identified at least the intermediaries, small interfering RNA (siRNA) that enact the methylation in the differing tissues. Which is why the biological pathway involving them has been termed the RNA-directed DNA methylation (RdDM) pathway. That still didn’t get us the answers we were seeking, however, as that just leads to the question of what’s regulating that pathway.

Since much of biological science works from the end products of such systems, we have learned quite a lot on just how the siRNA physically causes the DNA methylation and all the other genes and proteins they act upon, including non-coding RNA and methyltransferases. Which is useful to know and something we can at least partially manipulate. Though it would still be so much easier if we could alter things even further upstream. That led to a focus on understanding the parts that make up the RNA polymerase complex, as it also regulates and acts on methylation patterns. 

Classifying CLASSY

And that’s where prior research from the Salk Institute scientists came across the CLASSY genes that produce protein products involved in directing the polymerase to target DNA based on methylation. So, the four CLASSY proteins are the culprit. However, that 2018 study only identified them, it didn’t explain how this interaction then results in different methylation patterns in different plant tissues. Which is what our current study focused on. 

Using GUS marker genes and constructs of the CLASSY gene that were then transgenically inserted into Arabidopsis lines using Agrobacterium, the tissues of the subsequent generation of the plant could then be stained to make the GUS expression visible in places where the individual CLASSY genes were also being expressed. This identified that they did not all work the same. While some tissues, such as flower buds, might show all four of the genes active, other tissues were more differentiated. Leaves mostly saw the first CLASSY gene and mature ovules mostly the third with a little of the fourth. 

So here was the answer. CLASSY genes regulate methylation of the plant cell genomes and depending on which ones are expressed and how strongly they are expressed in a tissues’ cells determines what genes are active and which are kept offline. This creates a vastly different epigenetic “landscape”, as it were, between the tissues and between specific cell types on a more individual level than was even expected before the experiment. Which means that if we can break down the individual impacts of the CLASSY genes on cell types and how different levels of expression of each of the genes causes changes to regulation, we can that much more easily manipulate the growth and development of plants without external actions being required. 

Opening Doors of Regulation

The potential this has for improving seed yield (and getting rid of known negative impacts on seed development and longevity that certain epigenetic patterns have been shown to cause), along with general development of plants, can’t be understated. This could also allow us to directly create generations of plants with active resistances to stresses, such as drought or heat, improving their ability to survive in the future climate crisis of our planet. The extent of how useful the CLASSY genes will be in this regard are yet to be seen, but we can be hopeful that this new understanding will contribute to the ever growing knowledge base that biological research is developing.

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Photo CCs: Arabidopsis thaliana PID1137-3 from Wikimedia Commons

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