Transcriptional landscaping in plant stem cells: from chromatin to gene regulatory networks

All terrestrial life ultimately depends on plant meristems - small groups of undifferentiated cells that produce all major
plant organs such as leaves and flowers. In the shoot apical meristem (SAM) of higher plants such as Arabidopsis, gene
regulatory networks (GRNs) control cell growth, fate and identity to balance the formation of new organs, such as leaves
and flowers, with maintenance of meristem integrity, ensuring the sustainable supply of pluripotent cells necessary for
growth. Transcription factors, particularly the homeodomain protein SHOOT MERISTEMLESS (STM), play critical roles in
SAM function through regulation of target gene expression. However, the components and structure of the STM GRN are
not fully understood.
This project aims to develop a comprehensive understanding of the STM gene regulatory network in the SAM. STM
encodes a Knotted1-like TALE homeodomain transcription factor that is expressed only in the meristem. Loss of STM
function leads to failure to develop or maintain the meristem, while STM overexpression inhibits leaf cell differentiation
and promotes the de novo formation of ectopic shoot meristems. These dramatic phenotypic changes suggest a central
role for STM in the GRN(s) that regulate meristem development and function.
To understand how STM operates and how its role is integrated with the wider meristem GRNs, a multi-layered
transcriptional landscaping approach will be undertaken. First, putative STM target genes will be identified using inducible
STM overexpression and RNAi (gene silencing) followed by genome-wide RNA-seq analysis. In order to determine which
of these STM-responsive genes are directly regulated by STM, global chromatin immunoprecipitation (ChIP-seq) will be
performed to identify genomic regions to which STM is bound. Since STM also affects the chromatin structure to control
the differentiation status of cells, chromatin particle spectrum analysis (CPSA) will be used to analyse the chromatin
structure in the genomic regions bound by STM, placing the putative STM binding sites within the wider landscape of
nucleosomes and other DNA-bound factors. Bayesian network analysis will then be used to infer GRN structure and
relationships among the STM target genes.
This project is exciting opportunity to train under the supervision of two established experts in meristem biology, and to
learn multidisciplinary skills and techniques including molecular genetics, plant cell and tissue culture, bioinformatics and
developmental biology. The project will lead to new insights into networks controlling meristem development and could
lead to novel strategies for the manipulation of plant growth, architecture and yield.