Going Green: reprogramming roots into shoots using TCP transcription factors

As cells differentiate, their capacity to switch fate becomes progressively limited, which poses a problem for repairing
tissues and organs. Unlike other multicellular organisms, plants are known for their developmental plasticity. For
example, shoot cuttings can regenerate root systems and vice versa. During regeneration, plant cells have the unique
capability to change their identity by reprogramming their fate, a key mechanism in their ability to regenerate organs and
tissues. Cell fate reprogramming requires changes in gene expression, which in turn requires changes in chromatin
accessibility so that different genes can be accessed by the transcription machinery. Crucially, some transcription factors
called pioneer factors can bind inaccessible chromatin and change its conformation so that other factors can
access the DNA to initiate transcription, changing gene expression and causing cell reprogramming to a different fate.
Ectopic overexpression of a plant transcription factor, TCP4, drives the conversion of Arabidopsis roots into shoot/stem-
like organs, indicating that TCP4 has a central role in plant cell reprogramming. TCP4 regulates the expression of
several chromatin remodellers, which suggests that TCP4 has a broader role in controlling the chromatin landscape and
might be a novel plant pioneer factor.
To understand how TCP4 reprogrammes root cells, a combination of next generation sequencing techniques,
bioinformatics, and live cell imaging in inducible TCP4 lines will be used to obtain a comprehensive picture of the TCP4-
induced switch in cell fate. Chromatin maps from different timepoints of the root-to-shoot conversion process will be
obtained through the use of chromatin particle spectrum analysis (CPSA) and chromatin immunoprecipitation (ChIP-seq).
These maps will be compared to global changes in gene expression (RNA-seq) induced by TCP4 at the same timepoints to
identify regions of the chromatin that may have been made accessible by TCP4 to initiate gene expression. The
conversion of roots into shoots will also be monitored using fluorescent labels that allow us to recognise cell identity
by confocal microscopy. This will help us understand the mechanisms that allow TCP4 to reprogramme roots and will
contribute to establishing general principles of plant cell reprogramming.
This project is an exciting opportunity to learn multidisciplinary skills and techniques with wide applications. The
project will lead to new insights in regulation of transcription and pioneering activity in plants and could lead to
developing more efficient methods of plant propagation for sterile species, from a wider range of tissues, and provide
new strategies for improving agricultural traits and food security.