Role of chromatin fiber structure in genome function

Genomes are confined in the tiny, micrometer sized nuclei of eukaryotic cells, where they are highly compacted and at the same time constantly accessed by the cellular machinery that interprets the genomic information to produce the building blocks that the cell needs. During cellular division, the genome needs to duplicate and segregate rapidly and completely. These extraordinary features highly depend on the three-dimensional structure of the genome and on its packaging material called chromatin. We know that the wrapping of DNA into nucleosomes, the basic units of genome organization, has a great impact on all nuclear processes. Also long-range interaction between genomic regions are becoming better and better understood, and are particularly important in complex pathways of regulation. Knowing how the genome functions in a three-dimensional space is crucial for understanding how cells adapt to the environment, how multi-cellular organisms develop and for understanding the mechanisms causing disease. This proposal aims at elucidating the poorly understood area of how nucleosomes are structured inside the chromatin fiber in a genomic context and how this folding is implicated in genome function. The applicant is world-renowned for his track record on understanding chromatin fiber folding. Together with international collaborators who are experts in genomic applications, his team will use the latest generation methods of genomics and genetics to establish new tools that extend our capabilities of understanding the structure and function of eukaryotic genomes.

Genomes of eukaryotic cells rely on packaging by histone proteins into nucleosomes to manage the extremely long and charged DNA polymer in the confines of the cell's nucleus. Nucleosomes play a crucial role in gene regulation as general repressors and as substrates of epigenetic marks. They are further deeply involved in processes of DNA repair, replication and segregation. Nucleosomes cover the entire genome and form the chromatin fiber. The fiber organizes in preferentially interacting kilo- to megabases sized domains, in animals known as topologically associated domains (TADs), which confine long-range genomic interactions and thereby control promoter-enhancer interactions for example. However, the mechanisms that act on the chromatin fiber at the level of poly-nucleosomes, between the mono-nucleosomal and the genomic domain level, remain very poorly understood because the structure of the chromatin fiber in a genomic context is highly variable and is impossible to predict from the ideal chromatin fiber structures determined in vitro. It is therefore key to map the poly-nucleosomal configurations of the chromatin fiber at the genome-wide level. The applicant and his lab have determined several tetranucleosomal structures in vitro that provide a glimpse of the variability of poly-nucleosomal structures that await discovery in the genome. This research proposal seeks to establish a tool to map poly-nucleosomal architecture of the chromatin fiber genome-wide, and to apply this tool in order to discover the genomic mechanisms and functionalities acting at the poly-nucleosomal level. To this end this study will establish an integrated effort using chemical biology, biochemistry, genetics and genomics.

Disseminate research outcomes
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The fundamental questions addressed in this research project will have a direct impact on the field of chromatin and epigenetics. This research will answer a fundamental, long-standing question about the structure and function of the chromatin fiber. Peer review papers will be deposited with the Leicester Research Archive, a digital collection of research outputs from members of the University of Leicester (https://lra.le.ac.uk).

The PI and the postdoctoral research associate will attend international conferences during the period of support to present results and disseminate the new findings from the proposed research. For example, Dr Schalch has been contributing to the Cold Spring Harbor Chromatin Conferences, the Gordon Conference on Chromatin Structure and Function and has recently organized an EMBO conference on the Nucleosome.

Details of the research suitable for a lay audience will be contributed to LE1, the magazine of the University of Leicester, which is distributed locally and accessible for download. Dr. Schalch has his own web page (https://www.schalchlab.org), which contains research interests, achievements and information on publications. Outputs of this project will be added to the websites with commitment to keeping the information current, and will also be disseminated through social media like Twitter and Facebook.

Engagement with the press
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Engagement with the press will be coordinated through the press offices of the University of Leicester.

Engagement with schools
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The PI and postdoctoral research associate will participate in outreach activities organized by the Centre for Excellence in Teaching & Learning in Genetics (GENIE) to explain biomedical science to schoolchildren and other visitors; over 100 opportunities are available annually. This will include participation in the annual `Dynamic DNA' event held in the teaching laboratories at the University of Leicester and visited by approximately 600 children from local schools.

Dr Schalch will regularly engage with prospective students and parents at annual University Open Days.

Exploitation and application
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The University of Leicester has a vigorous and experienced Enterprise & Business Development team and an embedded unit `The Biobator', dedicated to exploitation of activities arising from work in biomedical research. Dr Schalch and his postdoctoral research associate will meet with their enterprise office regularly through the period of this grant to explore potential routes to commercial opportunities associated with the generation of their structural and functional data. This will allow having mechanisms in place to optimize the commercialization/intellectual property of the work and in this way allow timely publication of the results for the wider academic community.