Plant genomes are riddled with “jumping genes” that can copy themselves across the plant genome. Left unchecked, these so-called transposable elements disrupt and damage the genome. To silence these troublemakers, plant use a form of regulation called epigenetics, in which chemical tags on the DNA act as switches to control gene activity – effectively silencing transposable elements and preventing them from jumping. But how epigenetic markers are maintained every time a cell divides has remained unclear.

New research, led by Pierre Bourguet at the Gregor Mendel Institute (GMI) of the Austrian Academy of Sciences and published in Nature Plants, has now identified a new key player: a previously unknown protein called CDCA7. Working together with another protein, DDM1, CDCA7 is essential for one particular type of epigenetic modification, called CG methylation. The study was a collaborative effort with Eriko Sasaki of Kyushu University and was supervised by GMI group leader Frédéric Berger.

New insights into a key epigenetic factor

Heterochromatin is the tightly packed form of DNA in which genes are kept quiet. In plants, this tight packing is maintained by the protein DDM1. DDM1 is known to be essential for keeping different epigenetic marks in heterochromatin – but how DDM1 performs these multiple functions has remained unknown.

Bourguet and colleagues set out to understand DDM1 more deeply by identifying which proteins it works with. Thereby, they uncovered CDCA7 as a previously uncharacterized player in plant epigenetics. In plants, DDM1 and CDCA7 work together and form a complex. This complex specializes and is primarily responsible for directing a specific silencing tag called CG methylation.

This finding was key to separate DDM1’s multiple roles in epigenetics – like identifying the different tools of a Swiss army knife. “When DDM1 works together with CDCA7, it focuses on CG methylation, as we show here”, Pierre Bourguet explains. “For its other functions, DDM1, by extension, likely works with other protein partners.”

Linking epigenetics to natural variation

Beyond the molecular mechanism, the researchers also found that CDCA7 contributes to variation in epigenetic patterns. While methylation is maintained from one cell division to another, the level of methylation at transposable elements can vary between populations and individuals. “Variation in DNA methylation in different populations correlates with genetic variants in the promoter region of CDCA7”, explains Pierre Bourguet. In these variants, CDCA7 is more or less active, which in turn affects how strongly the genome is methylated.

By linking a precise molecular mechanism to natural variation, the study reveals how genetic diversity shapes the way plants maintain their epigenetic code. “In effect, natural variations in the CDCA7 gene act like a rheostat to adjust DNA methylation levels, allowing different plant populations to fine-tune their defences and protect their genome from the internal threat posed by transposable elements”, Pierre Bourguet says.

Differences in DNA methylation have also been linked with life history traits such as seed size, which is critical for survival in harsh environments. CDCA7 could therefore play a role in allowing plant populations to adapt to their local climate through variations in the epigenome.