Previous work

Chromatin accessibility and transcriptome changes during the evolution of polyploidy in Arabidopsis arenosa

Polyploid plants arise from whole-genome duplication (WGD) events, which have played important roles in genome evolution across eukaryotes. But how does the cell immediately respond to genome doubling, and how do these responses stablise over evolutionary time?

Here, we found that newly‐formed autopolyploids of A. arenosa show a burst of gene-expression and chromatin changes that further change in evolved natural polyploids, occasionally reverting to their ancestral diploid states.

Epigenomic consequences of knocking out MET1 in 18 A. thaliana accessions

By knocking out the CG-methyltransferase MET1 in multiple natural Arabidopsis thaliana strains, we showed that when CG methylation is broadly erased, the transcriptional responses and chromatin accessibility patterns diverge—suggesting that methylation helps stabilize (“canalize”) gene expression across genetic backgrounds.

Transcriptomic changes accompanying pollen tube growth defects in neopolyploids

Here, we showed that newly formed polyploid plants of Arabidopsis arenosa suffer infertility because their pollen tubes grow abnormally. Interestingly, two genes carrying genetic variants specific to evolved natural polyploids can rescue these defects. Furthermore, some of these defects can also be explained by expression changes of certain candidate genes involved in pollen tube growth and calcium signalling.

Epigenomic determinants of somatic mutation rate

In this collaborative work, we showed that mutation rates in plants are far from uniform across the genome. In Arabidopsis thaliana, epigenomic and physical features explain over 90% of the variability in where somatic mutations occur, and those patterns closely predict patterns of natural polymorphisms.

How stress facilitates phenotypic innovation and epigenetic diversity

In this opinion article with Hajk Drost, we explored how stress may not only challenge plants, but also bring opportunities for novel traits by modifying the epigenetic and genetic landscape, both within and across generations.

Origins and functions of plant epialleles

In this review with Anjar Wibowo, we took a deep dive into how epialleles (heritable epigenetic states) arise in plants, how they get established and maintained, and to what extent they regulate gene expression.