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 an 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.
*Please note that in their first year of the 4-year programme, DTP students will undertake taught units and rotation projects*
Eligibility Criteria
Applicants for a studentship must have obtained, or be about to obtain, a First or Upper Second Class UK Honours degree, or the equivalent qualifications gained outside the UK, in an appropriate area of science or technology. Applicants with a Lower Second Class degree will be considered if they also have a Master’s degree or have significant relevant research or non-academic experience.
In addition, due to the strong mathematical component of the taught course in the first year and the quantitative emphasis in our projects, a minimum of a grade B in A-level Maths or an equivalent qualification or experience is required (this includes a Physics A-level (grade B and above) or having undertaken units as part of your degree that have a significant mathematical component such as maths, statistics, bioinformatics. Applicants must ensure they highlight their Maths background within their application and to upload any supporting evidence.
To support PhD training opportunities, these studentships are only available to applicants that have not previously obtained or about to obtain a PhD degree (or equivalent).
If your first language is not English, you will need to meet the minimum English requirements for the programme (IELTS must be 6.5 overall and 6.5 in all sub-skills). Please note that the English Language requirement is stipulated by the University of Bristol, because of the first year taught elements, which is higher than is standard for Cardiff. We ask that the language requirements are met by 1st June at the latest, to allow adequate time to obtain any necessary documentation to allow you to study in the UK.
For more information about eligibility requirements, please visit: Eligibility – SWBiosciences Doctoral Training Partnership
How to Apply
To submit a formal application via Cardiff University’s online application service, click the 'Institution Website' button on this advert; in the ‘Apply’ box at the top-right of the page, select Qualification (Doctor of Philosophy), Mode of Study (Full Time) and Start Date (October 2022). This will take you to the application portal.
To apply for BBSRC SWBio studentships, candidates must submit the following:
Two references
Academic transcripts / degree certificate(s)
Personal statement. Please include supporting evidence for your Maths background.
Curriculum Vitae (CV)
English language certificates (where applicable)
NB: It is essential that students submit all the application elements required, as these will be needed for the shortlisting and interview processes.
In the research proposal section of the application, specify the project title and supervisors of the project. In the funding section, select “I will be applying for a scholarship/grant” and specify advertised funding from BBSRC SWBio DTP. If you are applying for more than one Cardiff University project, please note this in the research proposal section as the form only allows you to enter one title.
For more details on how to apply, visit the SWBio DTP website.
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