Dr Matthew Naish

Supervisor Details

Contact Details

Dr Matthew Naish

School of Life Sciences, University of Warwick

Scientific Background

Research Interests

In my lab, we explore how the genome’s architecture is regulated and inherited, focusing broadly on chromatin, the protein DNA complex that packages DNA. We are particularly interested in centromeres (specialised chromosome regions essential for accurate chromosome segregation) and use them as a model locus to investigate how unique chromatin domains are established, maintained, and regulated. By studying how centromeric chromatin is specified and preserved, we aim to uncover how these structures promote genome stability and ensure the faithful inheritance of genetic information. To address these questions, we use a combination of cutting-edge functional genomics, long-read DNA sequencing, live cell imaging and epigenomic approaches. Leveraging the powerful genetic tools and fully sequenced genomes of the model plant Arabidopsis thaliana we can dissect the molecular factors that define centromere identity and function.

Supervision Style

In three words or phrases: Curiosity-driven, collaborative and outcome-oriented

Provision of Training

This will initially led by myself at the bench. Specific equipment training provided by Research Technology Platforms (RPTs). As you progress I also encourage students to be proactive in seeking training and development opportunities with others in the department and University as a whole.

Progression Monitoring and Management

Lab members are expected to take ownership of their projects and act as the main driving force behind them. As we are a small lab, we discuss your projects regularly — through informal weekly conversations and a more formal lab meeting, where members present on a rotational basis. You should keep me updated on new results, challenges, and plans. Based on your progress, I will provide advice and guidance to help steer your project toward the best outcomes. I will also outline my expectations for your development on a monthly basis.

Communication

I am always available to be contacted by email, additionally we use ‘Slack’ for communicating within the group and use this as a platform to share files, documents and updates.

Meetings

PhD Students can expect scheduled meetings with me at least once per week. These meetings will be face-to-face. I am usually contactable for an instant response on every working day.

Work Patterns

The timing of work in my lab is completely flexible, and (other than attending pre-arranged meetings) I expect students to manage their own time.

Notice Period for Feedback

I need at least 2 weeks' notice to provide feedback on written work of up to 5,000 words.

MIBTP Project Details

Primary supervisor for:

Connecting Centromere Diversity to Chromosome Transmission

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

Connecting Centromere Diversity to Chromosome Transmission

Secondary Supervisor(s): Professor Andrew McAinsh

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

Every time a cell divides, its chromosomes must be accurately divided to ensure the new cells inherit the full set of genetic information. The 'anchor points' that facilitate this are called centromeres which load a multi-protein structures called kinetochores. While centromeres have the same essential function, the underlying DNA is some of the most rapidly evolving regions of the genome. Advances in long-read sequencing has allowed the complete assembly of these regions and has revealed remarkable diversity even between closely related accessions of Arabidopsis thaliana. However, how this diversity shapes centromere and kinetochore organisation and function remains a key question.

Arabidopsis hybrids containing diverse centromere structures show distorted inheritance of some chromosomes. This interdisciplinary project will investigate how different centromere structures influence chromosome behaviour during cell division. This project will use Nanopore sequencing, proteomics, and cutting-edge live-cell imaging approaches to study how changes in the centromere structure, or composition influence the way chromosomes move and during cell division.

Objectives

1) Explore how variation in centromere DNA sequence and chromatin organisation affect chromosome movement.

2) Use live imaging to track their attachment to the spindle poles during division.

3) Investigate the link between sequence diversity to functional outcomes, and build a model that connects centromere structure to chromosome behaviour.

This project will give you experience in genetics, advanced microscopy, and quantitative image analysis, at the interface of plant and chromosome biology. The results will advance our understanding of how chromosomes faithfully transmit genetic information, addressing a fundamental question in biology.

Wlodzimierz P et al. https://doi.org/10.1038/s41586-023-06062-z

Nicola Gorringe, et al https://doi.org/10.1101/2025.01.04.631303

How are Centromeres Established? Chromatin and Neo-Centromere Seeding in Plants

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

How are Centromeres Established? Chromatin and Neo-Centromere Seeding in Plants

Secondary Supervisor(s): Professor Jose Gutierrez-Marcos

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

Every time a cell divides, its chromosomes must be accurately separated to ensure the new cells inherit the full set of genetic information. The "anchor points" that allow chromosomes to attach to the division machinery are called centromeres - which load a specialised multiprotein complex called the kinetochore. The functional centromere is specified epigenetically through incorporation of a centromere-specific histone variant (CENH3). Where a centromere forms on a chromosome influences key biological processes, such as suppressing meiotic recombination, which can shape the genetic potential available for crop breeding.

Despite their essential function centromere locations can migrate to new regions on a chromosome, but the mechanism by which this occurs is unclear. In Arabidopsis, only certain parts of the repetitive centromeric DNA are "active" (loaded with CENH3), while neighbouring repeats remain "silent". This multidisciplinary project will explore what distinguishes these "active" sites within the centromere, how chromatin states define centromere stability, and use engineering biology approaches to seed the active centromere at new genomic locations.

Objectives

1) Nanopore long-read sequencing and epigenomic profiling to map chromatin modifications across centromere regions.

2) Proteomics and mutant analysis to identify factors that stabilise active centromere sites.

3) Engineering biology approaches (CRISPR-based tethering systems such as SunTag) to artificially recruit CENH3 and regulators to new genomic loci, to seed functional neo-centromeres.

This exciting project will give you training in genetics, genomics, and engineering biology, and will address fundamental questions in chromosome biology with long-term potential for engineering plant centromeres for use in crops.

References

Naish M, et al., (2021) Science. 374:eabi7489.

Naish, M. (2024), New Phytol, 244: 2143-2149. https://doi.org/10.1111/nph.20149