Regulation from a distance
Listening to talks from animal researchers about gene regulation I always was a bit worried that I was missing something about this in plants. Because in the animal genome regulatory elements, that tell gene regulators when a gene needs to be turned on, lay quite far away from the genes they regulate. Gene and regulatory elements can easily be millions of bases apart.
In plants this is not the case. There, the promoter, the bit of sequence in front of the gene which is needed for turning the gene on or off, is often relatively short, a couple of thousands of bases at most. Now a new study “Two deeply conserved non-coding sequences control PLETHORA1/2 expression and coordinate embryo and root development” shows that plants also have those gene regulatory elements.
To find out if plants contain those gene regulatory elements, or conserved non-coded sequences as they are called, a group of Dutch and American researchers analysed a stretch of 20 000 bases in front of the PLETHORA genes from 120 plant species. PLETHORA genes are master regulators of plant development. And as such they are particular well conserved among plants.
Needed for expression
Two stretches of DNA stood out. The first one, named BOX1, is closest to the start of the PLETHORA genes and spans about 90 bases. The second one, about 100 bases further away the researchers called BOX2 and spans about 60 bases. Both stretches of DNA occurred almost identically in almost all species analysed.
To check if this are indeed regulatory sequences the researchers did what researchers do. They deleted BOX1, BOX2, or both. Finding that both stretches of DNA where needed for the expression of the PLETHORA 1 and 2 genes. In addition, the roots of plants without BOX1 and/or BOX2 did not grow or only verry slowly. Clearly indicating that the BOX1 and BOX2 are needed for proper expression of PLETHORA 1 and 2 and for root growth.
Next the researchers looked at where in the root PLETHORA is expressed and how BOX1 and BOX2 influences this. By coupling the PLETHORA with a fluorescent tag, the researchers found that in the absence of BOX1 PLETHORA is no longer seen in the root growth centre. Whereas absence of BOX2 stops PLETHORA being active in the vascular tissue. The researchers not only noticed this in seedlings, but also for developing embryos.
Better access
The following question the researchers liked to answer was of course: How do BOX1 and BOX2 elements regulate gene expression? The first hint they got when looking to how accessible the DNA was. They found that especially in growth centre regions of the plant BOX1 and to a lesser extend BOX2 allowed better access to the DNA. This in turn suggest that there is something that keeps the DNA accessible at those places, the most likely culprits for that are transcription factors, a.k.a. gene regulators.
Hints for which gene regulators, the researchers found by looking at the sequence of BOX1 and BOX 2. This revealed that they contain patterns to which PLETHORA proteins bind. Yes, you read that right. The PLETHORA proteins bind to the regulatory elements of their own genes. Creating a so called autoregulatory feedback loop.
Now this is one study and with the conformational work done in the lab rat under the plants: Arabidopsis. However, it wouldn’t surprise me if in addition to regulatory patterns to which gene regulators bind, plant genes also have those longer stretches of regulatory elements.
Literature
Kerstens, M., Boele, Y., Moralez-Cruz, A., Roelofsen, C., Wang, P., Baumgart, L.A, O’Malley, R., Sanchez-Perez, G., Scheres, B., Willemsen, V., Two deeply conserved non-coding sequences control PLETHORA1/2 expression and coordinate embryo and root development, Plant Communications (2025), doi: https://doi.org/10.1016/j.xplc.2025.101466.
Plant en Zo 