Research

The groups research is currently focused in three main areas:

Epigenome-engineering the primed state:

Schematic of defense priming and the potential for epigenome engineering to ‘vaccinate’ plants.
CRISPR based SunTag tool for precise epigenome engineering. see link.

Plants are able to respond more rapidly and robustly to stress if they have been previously challenged. This indicates that a memory of the initial stress is retained. Plants lack a brain, but can store ‘epigenetic memories’ in chromatin. Understanding the details and dynamics of this process could have major implications for agriculture and lead to the ability to precisely re-sculpt chromatin so that plants are primed, resilient and robust to challenge. To this end, we are 1) mapping chromatin in the ‘memory’ state (histone modifications, accessibility, DNA methylation) 2) identifying the genetic factors required for priming / memory, and 3) developing CRISPR based epi-genome engineering approaches to re-sculpt chromatin.

Reading the chromatin landscape:

Schematic overview of ‘molecular fishing’. Tissue from the model plant Arabidopsis is collected, nuclear proteome is extracted and incubated with different post-translationally modified peptides as ‘bait’, and mass spectrometry is used to identify the nuclear proteins that bind them. We collaborate with mass spec experts to perform these experiments.

Chromatin state varies widely across the genome, providing critical information about the underlying DNA elements. There are a vast array of chromatin marks and modifications, yet our understanding of their function lags far behind. One of the best ways to reveal the function of particular marks is to identify the factors in the cell that are able to perceive or read them. Comparative interactomics is a powerful ‘molecular fishing’ approach that facilitates the identification of these epigenetic readers. Working with world experts in quantitative mass spectrometry, we are using this approach to reveal the readers of key chromatin marks. Once identified, we study their function using an array of genetic, genomic, biochemical and informatic approaches.

DNA methylation and transcriptional activation:

The DNA methylation reader and activator complex. see link.

DNA methylation has a complex relationship with transcription. It is normally associated with repression, but in certain contexts, DNA methylation is required for transcription. We previously identified the first molecular complex that directly links DNA methylation to transcriptional activation. This complex consists of the DNA methylation reader proteins SUVH1 and SUVH3, and the transcriptional activator proteins DNAJ1 and DNAJ2. Because transposable elements are marked by methylation for silencing, this complex is thought to help protect the expression of genes if a transposon inserts nearby. Crop genomes often have unusually high transposable element content, and so this complex could help to ‘unlock’ genomic regions from silencing, leading to novel avenues for agricultural improvement. However, major questions remain. How does DNAJ1/2 induce transcriptional activation? Where do DNAJ1/2 exist in the nucleus and what do they interact with? How does DNAJ1/2 differentiate between transposons (which must remain silent) and important genes (which must remain active)?

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