Transposable Elements are fragments of DNA that can move themselves from one place in a genome to another, creating mutations and potentially genome instability. To control transposable elements, eukaryotic cells target them with chromatin modifications and/or DNA methylation to repress their transcription, and this regulation can be heritable (epigenetic). The Slotkin lab's long-term goal has been to understand how plant cells first recognize transposable elements and trigger the cycle of chromatin modification and epigenetic silencing. We have used the transfer of foreign transposable elements from other plant species and fungi into the reference plant Arabidopsis to study the de novo initiation of epigenetic silencing, and through this process uncovered how to keep a foreign transposable element active in a plant genome. This control over transposable element activity is useful for genome engineering, as we can now control the activity, insertion site, cargo and timing of transposable elements in Arabidopsis and the major crop Soybean. Using transposable elements and a programmable nuclease such as Cas9 has provided us newfound control over transposable elements and the evolutionary processes they drive. 

One of the most striking, yet poorly understood, forms of plant movement is the climbing capacities of woody vines, also known as "lianas". These plants weave through the forest, attaching to host branches as they grow towards light at the top of the canopy. Surprisingly, this complex and unusual phenotype has independently evolved in at least one-third of vascular plant families and can represent upwards of 40% of the leaf area in tropical forests. Thus, the ability to climb is a strategic lifeform in the evolution of plants to compete for light. Despite the evolutionary and ecological significant of lianas, we still lack an understanding of how plants evolved to climb.

In this talk, I will present a multi-scaled approach to elucidate the evolution and development (evo-devo) of cells and phylogenetics, developmental anatomy, comparative transcriptomics, to cell wall biology. I begin by discussing the role of "vascular variants" i.e., aberrations in the distribution and abundance of vascular tissues, in the large neotropical liana tribe, Paullinieae (Sapindaceae). I will conclude by discussing our ongoing efforts to elucidate the developmental mechanism underlying twining motion of common bean vines, through hormonal perturbation, RNA seq, and our efforts to understand the link between microtubule orientation and whole-form architecture.

The Strader lab has been studying transcriptional output of the Auxin Response Factors, key regulators of plant growth and development, finding that protein condensation, nucleo-cytoplasmic partitioning, and activation domain activity can be modulated to integrate environmental and developmental cues into their transcriptional activity.

Plant researchers have long sought to engineer endogenous gene regulation to improve crop traits, and to insert into crops multi-gene cassettes that encode metabolic pathways for bioproducts. However, we lack sufficient knowledge of the functional elements directing gene expression and the ways in which they interact – the regulatory grammar – to make the engineering of crop traits and pathways routine. Thus far, predicting the expression in plants of synthetic genes and pathways, even those composed of well-characterized DNA sequences, remains a major challenge. Indeed, when individual pathway genes are assembled into larger designs, their performance shows strong context-dependent properties. Moreover, our current tool set contains only a handful of regulatory elements, often of bacterial and viral origin, that constitutively and ubiquitously drive gene expression, contributing to expression interference, silencing and reduced crop fitness. Thus, new approaches are needed to engineer programmable and tunable gene expression. Our team has pioneered Plant STARR-seq, a reductionist but highly versatile MPRA, to test the activity of hundreds of thousands of regulatory elements in a dicot and a monocot system. The large scale of the resulting data allows for machine learning and in silico evolution of regulatory elements with desired features. I will discuss our recent efforts to understand insulators and silencers in plant genomes.

Genome-scale regulatory landscapes and long-range regulatory interactions are typically inferred from short-read data. To resolve the context-dependency of gene regulation, we need to move beyond averaging large numbers of small fragments that are mapped back to the genome; instead, we need to explore the regulatory events that occur simultaneously on single chromatin fibers. We have adapted Fiber-seq, a long-read single molecule method, for use in plants. Fiber-seq of maize leaf protoplasts faithfully recapitulates regulatory elements found in matched ATAC-seq samples and finds new elements. I will present results on regulatory activity in LTR retrotransposons, and show that Barbara McClintock’s discovery of transposon mobility may have been aided by less rigidly packed chromatin at these specific loci.