Read the Publication

This week we profile a recent publication in the Plant Cell from
Dr. Josh Cuperus (right) and Ken Jean-Baptiste (left) at the University of Washington.

Can you provide a brief overview of your lab’s current research focus?

Our group focuses on gene regulation in plants. About half of the known domestication or trait improvement events in crops have been due to regulatory DNA changes resulting in changes in gene expression. While recent advances from our group and others have uncovered the regions of the genome that are accessible, i.e. where transcription factors bind, we really don’t know which of these regions confer changes to expression. Therefore, functional assays to identify true enhancers is a major direction we are pursuing. We are also interested in identifying and manipulating gene expression in single-cell types. This will include using new technological advances in single-cell ‘omics technologies.

What is the significance of the findings in this publication?

In this study we have uncovered the expression architecture for an entire plant organ, the root system. Using single-cell RNA sequencing we can answer new questions involved in the gene expression in Arabidopsis roots. Plants, unlike most other organisms, have a constant body plan, where new cells are being made in the meristematic regions continuously. This feature allows us to measure development of cell types over time, capturing both new cells and older cells. We used these developmental trajectories to identify age-dependent transcription factor motifs and watch terminal cell differentiation occur with decreases of general transcription but drastic increases in cell-type specific genes over development. Overall our findings act as a gateway to understanding the entire root system architecture in a single experiment.

What are the next steps for this research?

While Arabidopsis is a great starting place for our research, we hope to apply this to crop species to help us guide altering root system architecture to create crops better suited for abiotic stresses or nutrient uptake. There are several challenges to applying single-cell methods to crops, including more complex root cell-types, and fewer genetic tools, however the work we have established here should help us in this endeavor. We have also begun applying this methods to above ground tissue, measuring single-cell gene expression in both leaves and shoots.

This research was funded by:

National Science Foundation
MCB-1516701
RESEARCH-PGR 1748843

National Institutes of Health
U54DK107979
DP2HD088158
RC2DK114777
R01HL118342
T32LM012419

Read the Publication