Role of chromatin fiber structure in genome function

Lead Research Organisation: University of Leicester
Department Name: Molecular and Cell Biology

Abstract

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.

Technical Summary

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.

Planned Impact

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.

Publications

10 25 50
 
Description Collaboration with Oliver Rando 
Organisation University of Massachusetts
Department University of Massachusetts Medical School
Country United States 
Sector Academic/University 
PI Contribution We are preparing samples for next generation sequencing analysis in order to map nucleosome-nucleosome contacts.
Collaborator Contribution Prof. Oliver Rando and his postdoc Nils Krietenstein run next generation sequencing on our samples and do bioinformatic analysis.
Impact We're in the early stages of the project and do not have tangible outcomes yet.
Start Year 2018
 
Description College of Life Sciences online Research Seminar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Online presentation of our research to the College of Life Sciences of the University of Leicester.
Year(s) Of Engagement Activity 2020
URL https://le.ac.uk/cls
 
Description Global Discussion Camp, Tokyo Metropolitan University 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact Thomas Schalch was part of a delegation from the University of Leicester with undergraduate students and colleagues, which visited Tokyo Metropolitan University (TMU) for a week-long workshop with TMU undergraduate students and professors. Thomas gave a lecture covering topics of the BBSRC grants. This activity sparked many new contacts and will likely lead to further exchanges between TMU and the Univeristy of Leicester.
Year(s) Of Engagement Activity 2019
 
Description Presentation at Telluride Workshp Epigenetic Mechanisms 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This Telluride Science Research Centre workshop in Telluride, Colorado, USA brought together internationally leading scientists who study molecular mechanisms of epigenetic mechanisms. Thomas Schalch presented as one of the speakers of the workshop.
Year(s) Of Engagement Activity 2019
URL https://www.telluridescience.org/meetings/workshop-details?wid=783
 
Description Seminar Thomas Schalch ETH Zurich 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Thomas Schalch presented a research seminar at the Department of Biochemistry at the ETH in Zurich. This visit sparked various discussions with faculty at the ETH that explored future collaborations related to our BBSRC grants.
Year(s) Of Engagement Activity 2019
 
Description Seminar Thomas Schalch LMU Munich 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Thomas Schalch presented a research seminar at the Biomedical Center Munich of the Ludwig-Maximilian University in Munich. This visit involved several discussions with faculty members of the LMU. This visit further consolidated our collaboration with the laboratory of Sigurd Braun.
Year(s) Of Engagement Activity 2019
 
Description Seminar Thomas Schalch The University of Tokyo 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Thomas Schalch presented a research seminar at the University of Tokyo hosted by Hitoshi Kurumizaka. During this meeting, Thomas Schalch met with various researchers and faculty from other Japanese Universities. This visit also further consolidated the collaboration of Thomas Schalch with Hitoshi Kurumizaka on the Chromatin conference we are organizing in Leicester, which is supported by our BBSRC Japan Partnering Award. The visit further provided an opportunity to explore opportunities for future collaborations.
Year(s) Of Engagement Activity 2019
 
Description Seminar Thomas Schalch University of Colorado Boulder 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Thomas Schalch presented a research seminar at the University of Colorado, Boulder. He had further several discussions with faculty that explored input and potential collaborations related to our BBSRC grants. This has in particular updated our technical approach to histone purification through discussions with members of the laboratory of Karoline Luger.
Year(s) Of Engagement Activity 2019
 
Description What do you want to be day? at Avenue Primary School 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact We have visited the Avenue Primary School in Leicester to demonstrate crystal growth and what proteins structures of chromatin and nucleosomes look in 3D. This event is designed to give pupils a flavor of the jobs and careers that are out there. Our visit has sparked great interest from the children, which spanned Years 1-6. We have been invited again this year by the School.
Year(s) Of Engagement Activity 2019