Professor Jose Gutierrez-Marcos

CASE: Control of Male Fertility in Plants through Exogenous Small RNAs

University of Registration: University of Warwick

Non-academic partner: Dr Federico Ariel (APOLO Biotech)

Secondary Supervisor(s): Professor Guy Barker

Project Outline

Sexual reproduction represents a critical bottleneck in plant life cycles, requiring faithful transmission of both genetic and epigenetic information. Small RNAs (sRNAs) are key regulators of germline integrity, repressing transposable elements and maintaining genome stability during the extensive reprogramming that occurs in reproductive tissues. Intriguingly, sRNAs are not only generated within cells but also move between them, acting as mobile signals that influence fertility. However, the mechanisms governing sRNA mobility and its functional impact on male reproductive development remain poorly defined.

This project will explore how exogenous sRNAs can be used to control male fertility in plants, with the long-term goal of providing tools for crop improvement. Specifically, it will address three fundamental questions: (1) What are the molecular routes and barriers for sRNA uptake and transport within anthers and developing germline cells? (2) How is the movement of sRNAs regulated, and can it be manipulated by external delivery of synthetic sRNAs? (3) What roles do mobile sRNAs play in controlling male fertility, and how can this be exploited to generate conditional male sterility?

The student will use an interdisciplinary approach combining plant genetics, synthetic biology, and advanced imaging. CRISPR-based reporters and fluorescent sRNA sensors will be used to track sRNA mobility in different tissues. Targeted delivery of exogenous sRNAs will test their ability to silence fertility genes, providing a direct proof-of-concept for controlling male fertility through mobile RNA signals. Finally, phenotypic analyses using automated imaging platforms will assess the impact on pollen development and fertility outcomes.

By uncovering how exogenous sRNAs can reprogram reproductive development, this project will provide fundamental insights into the rules governing intercellular communication, epigenetic inheritance and offer a novel strategy for hybrid seed production and crop resilience.

Inheritance of chromatin marks during cell replication in plants

Secondary Supervisor(s): Professor Daniel Hebenstreit

University of Registration: University of Warwick

BBSRC Research Themes:

• Sustainable Agriculture and Food (Plant and Crop Science)
• Understanding the Rules of Life (Plant Science)

Project Outline

The correct development of multicellular organisms requires the specification and maintenance of distinct cell types. These identities must be preserved through cell divisions, while genomic integrity is safeguarded during DNA replication. Genome duplication involves not only copying DNA but also faithfully replicating chromatin, the complex of DNA and histone proteins assembled into nucleosomes. Thus, both DNA and histones, along with their post-translational modifications (PTMs), must be accurately inherited by daughter chromatin. Because chromatin landscapes regulate gene expression, the transfer of parental histones and their integration with newly synthesised histones is critical to maintaining transcriptional memory after division. DNA methylation is known to be copied after replication through coordinated interactions with histone modifications.

Recent work links chromatin inheritance to the replication machinery, though the exact molecular mechanisms remain unclear. In plants, understanding is limited because most insights come from mutants in chromatin regulators or enzymes modifying histone PTMs, which often display pleiotropic defects. The precise machinery ensuring accurate chromatin transfer, and how it is recruited to specific genomic regions during replication, remains unknown.

This project addresses these gaps through three objectives:

1. Define the role of histone demethylases in balancing chromatin mark inheritance during replication using engineered conditional knockouts.

2. Identify molecular components involved in histone mark replication through targeted proteomics in cell cultures.

3. Apply super-resolution microscopy to track chromatin dynamics across the cell cycle and their association with the replisome, the complex that replicates DNA.

Collectively, this work will advance understanding of chromatin state inheritance in plants.

Mechanisms controlling transgenerational stress memories in plants

Secondary Supervisor(s): Professor Guy Barker

University of Registration: University of Warwick

BBSRC Research Themes:

• Sustainable Agriculture and Food (Plant and Crop Science)
• Understanding the Rules of Life (Plant Science)

Project Outline

Epigenetic mechanisms underpinning intergenerational memory are relatively well understood and involve high levels of H3K4me3 and RNAP II phosphorylation. In contrast, the mechanisms regulating transgenerational memory remain poorly defined. Our preliminary work shows that environmental signals not only influence plant growth but can also trigger phenotypic changes transmitted to progeny, although these rarely persist over multiple reproductive cycles. We found that stress induces stochastic changes in DNA methylation, inherited by offspring but actively removed by DNA demethylases during germline development. In addition, transgenerational memories are reinforced by transcription factor feedback and the histone demethylase REF6.

Using Arabidopsis, we developed a novel strategy to induce abiotic stress memories (extreme temperature and hyperosmotic stress) and identified genomic regions sensitive to epigenetic modification. Our data suggest these elements influence neighbouring gene expression by altering 3D chromatin architecture, though the underlying mechanisms remain unclear.

The project will address this through three objectives:

1. Define the role of stress-memory elements using CRISPR/Cas9 to generate targeted genetic and epigenetic changes and assess effects on transcriptional memory.

2. Assess how chromatin conformation contributes to stress memory by applying epigenome editing tools to modify chromatin landscapes at stress-memory elements.

3. Determine how genome modifications affect abiotic stress memory using automated phenotyping to track phenotypic dynamics following manipulation of stress-memory elements.

Together, this work will provide new insights into the epigenetic mechanisms of transgenerational memory in plants and deliver essential knowledge for engineering crops with enhanced stress resilience.