The ATRX programme

Lead Research Organisation: University of Oxford

Abstract

Despite the revolution in genetics in the last decade and in particular the sequencing of the human genome, the regulation of gene expression largely remains a mystery. Every cell of the body contains a full complement of genes but only expresses a small repertoire required for that tissues function, such as the oxygen carrying protein, haemoglobin, in red blood cells. A complex hierarchy of regulation is emerging involving tissue-specific signals, chemical modifications to the DNA molecule and the proteins about which DNA is wrapped, enzymes that package and unpackage DNA and different cellular compartments that either favour or repress gene expression. Human genetic diseases are now being identified in which the components of this complex apparatus are disrupted. In one such condition, ATR-X syndrome, the affected children have profound learning difficulties, a characteristic facial appearance, abnormalities of genital development and a form of anaemia. It arises because of mutations in a protein involved in the regulation of gene expression. The diverse problems probably reflect the many different genes whose expression is perturbed. The overall aim of this programme is to determine the role of such proteins in the regulation of gene expression and their involvement in human disease.

Technical Summary

In higher organisms, DNA is packaged in the cell nucleus as a protein /DNA complex, known as chromatin. In the last twenty years, the importance of chromatin-associated proteins in the regulation of gene expression has been established. One such class of proteins, chromatin remodellers, plays a role in altering the packaging and accessibility of DNA. Through the study of a form of syndromal mental retardation associated with a thalassaemia it is apparent that mutations in ATRX, a putative chromatin remodelling protein, can perturb normal a globin gene expression. The overall aim of this programme is to determine the role of such chromatin remodelling proteins in the regulation of gene expression and their involvement in human disease.||ATR-X syndrome comprises mental retardation, facial dysmorphism, urogenital and skeletal abnormalities and an unusual form of the anaemia, a thalassaemia. A thalassaemia arises when there is a defect in the synthesis of the a globin chains of adult haemoglobin (HbA, a2b2). ATR-X results from mutations in an X-encoded factor, ATRX. We have also shown that acquired, somatic mutations in ATRX are also associated with rare premalignant haematological condition, alpha thalassaemia myelodysplastic syndrome. Mutations in this gene down-regulate a gene expression and also perturb the expression of other, as yet unidentified genes.||To date, we have diagnosed over 150 cases of ATR-X and identified the mutations in majority of these. Analysis of these natural mutants has been one of the most powerful ways of elucidating the function of ATRX. In particular, it has helped define the phenotypic spectrum of the condition and the functional significance of predicted protein domains. Through this work we have collected an invaluable resource of patient cell lines and DNA samples which has facilitated our understanding of the pathophysiology of this condition. We will continue this diagnostic service through which potentially valuable and instructive new cases will be identified.||ATRX is a heterochromatic protein and mutations perturb the normal pattern of DNA methylation at diverse loci. In order to understand the role of ATRX in gene expression we need a better understanding of where and how ATRX is localised and the proteins with which it interacts and its normal repertoire of gene targets. We need a clearer idea of how ATRX effects methylation and the relationship of this to gene expression. We are developing model systems that are amenable to manipulation and allow us to more closely examine the role of ATRX in tissues (such as brain and bone marrow) not accessible in patients with ATR-X syndrome.||We have expressed the ATRX protein in vitro and can now start to analyse its function in a better defined and more precise manner. In addition we have developed a chromatin immunoprecipitation approach to identifying the direct targets of ATRX and thereby better understand how it identifies and modifies its targets. We are modifying DT40 cells and using mutants of the ATRX protein interaction domains to identify protein partners of ATRX. The widespread abnormalities in methylation in ATRX mutants presents one of the most intriguing puzzles. We plan to determine how mutations in ATRX produce abnormal patterns of methylation using newly developed models involving ES cells and iPS cells.||In order to understand the structural and functional consequences of the mutations that arise in the major protein domains, the structure of PHD-like domain has been determined in collaboration with Dr Daniela Rhodes (LMB, Cambridge). Further studies are underway to use these structures to analyse how ATRX may interact with chromatin.||Although the study of ATR-X patients has been extremely valuable in our initial understanding of the phenotype of ATR-X syndrome, for a thorough understanding of the role of ATRX and the pathophysiology associated with mutations of ATRX we require an animal model. We have been developed a mouse kn

Publications

10 25 50
 
Description ATR-X diagnostics
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
Impact Characterisation of an important inherited cause of learning difficulties. Development of diagnostic test for this condition including prenatal diagnosis.
 
Description BRC3 Haematology and Stem Cell
Amount £4,602,645 (GBP)
Funding ID BRC3 
Organisation National Institute for Health Research 
Department NIHR Biomedical Research Centre
Sector Public
Country United Kingdom
Start 04/2017 
End 03/2022
 
Description Capital Prioritisation for MRC Units and Institutes
Amount £75,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 04/2018 
End 03/2019
 
Description Characterisation of ATRX
Amount £1,836,569 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 04/2017 
End 03/2022
 
Description Characterisation of ATRX, a chromatin remodelling protein
Amount £1,870,606 (GBP)
Funding ID MC_UU_12009/3 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 04/2012 
End 03/2017
 
Description Daphne Jackson Fellowship
Amount £52,418 (GBP)
Organisation University of Surrey 
Department Daphne Jackson Trust
Sector Charity/Non Profit
Country United Kingdom
Start 05/2012 
End 04/2015
 
Description Determining the structure fo the ATRX tumour suppressor complex
Amount £15,000 (GBP)
Organisation Cancer Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2016 
End 03/2017
 
Description Exploring mechanisms of enhancer action in erythropoiesis
Amount £250,000 (GBP)
Funding ID 209181 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2018 
End 03/2022
 
Description FP7 Marie Curie ITN
Amount £230,000 (GBP)
Organisation Marie Sklodowska-Curie Actions 
Sector Charity/Non Profit
Country Global
Start 04/2010 
End 03/2013
 
Description Fp7 Marie Curie Network - ITN
Amount £213,151 (GBP)
Organisation Marie Sklodowska-Curie Actions 
Sector Charity/Non Profit
Country Global
Start 04/2009 
End 03/2013
 
Description Identifying suppressor mutations of ATR-X and ADNP syndromes using a novel CRISPR-based screening method in mice
Amount £250,000 (GBP)
Funding ID 210913 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 11/2018 
End 10/2022
 
Description MRC DTG - J TRUCH
Amount £41,915 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 10/2013 
End 09/2019
 
Description MRC DTP - J TRUCH
Amount £21,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 10/2018 
End 03/2019
 
Description MRC Molecular Haematology Unit
Amount £27,659,000 (GBP)
Funding ID MC_UU_12009 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 04/2017 
End 03/2022
 
Description The role of U2AF1 mutations in anaemia and haematological malignancies
Amount £10,000 (GBP)
Organisation Oxford Hospitals Charity 
Sector Charity/Non Profit
Country United Kingdom
Start 07/2018 
End 07/2021
 
Description WIMM - MRC Festival Establishment Award
Amount £3,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 02/2019 
End 03/2024
 
Description WIMM - WIMM MHU Capital Funding Award 2019/20
Amount £85,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 04/2019 
End 03/2020
 
Description Wellcome Trust Research Training Fellowship
Amount £211,702 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 07/2007 
End 06/2011
 
Title ATR-X syndrome cell line collection 
Description Cell lines from affected individuals 
Type Of Material Biological samples 
Year Produced 2006 
Provided To Others? Yes  
Impact Multiple publications 
 
Title ATR-X syndrome cell line collection 
Description Cell lines from affected individuals 
Type Of Material Database/Collection of Data/Biological Samples 
Year Produced 2006 
Provided To Others? Yes  
Impact Multiple publications 
 
Title ATRX monoclonal antibodies 
Description ATRX monoclonal antibodies 
Type Of Material Antibody 
Year Produced 2006 
Provided To Others? Yes  
Impact Multiple publications 
 
Title ATRX monoclonal antibodies 
Description ATRX monoclonal antibodies 
Type Of Material Antibody 
Year Produced 2006 
Provided To Others? Yes  
Impact Multiple publications 
 
Title Improved functional diagnostic test for ATR-X syndrome 
Description Development of a functional test for ATR-X syndrome based on abnormal DNA methylation 
Type Of Material Technology assay or reagent 
Provided To Others? No  
Impact Identification of ATR-X syndrome in individuals negative using previous tests 
 
Title Improved functional diagnostic test for ATR-X syndrome 
Description Development of a functional test for ATR-X syndrome based on abnormal DNA methylation 
Type Of Material Technology assay or reagent 
Provided To Others? No  
Impact Identification of ATR-X syndrome in individuals negative using previous tests 
 
Title Mouse ATRX knockout and floxed model 
Description Mouse ATRX knockout and floxed model 
Type Of Material Model of mechanisms or symptoms - mammalian in vivo 
Year Produced 2006 
Provided To Others? Yes  
Impact 17503331, 16628246, 19020049, 19088125, 20211137 
URL http://europepmc.org/abstract/MED/17503338
 
Title Mouse ATRX knockout and floxed model 
Description Mouse ATRX knockout and floxed model 
Type Of Material Model of mechanisms or symptoms - mammalian in vivo 
Year Produced 2006 
Provided To Others? Yes  
Impact 17503331, 16628246, 19020049, 19088125, 20211137 
URL http://europepmc.org/abstract/MED/17503337
 
Description Characterisation of ATRX function in mouse brain 
Organisation Western University
Country Canada 
Sector Academic/University 
PI Contribution Provided ATRX knockout and floxed mouse
Collaborator Contribution Characterisation of ATRX function in mouse brain
Impact 19020049
 
Description Characterisation of ATRX function in mouse brain 
Organisation Western University
Country Canada 
Sector Academic/University 
PI Contribution Provided ATRX knockout and floxed mouse
Collaborator Contribution Characterisation of ATRX function in mouse brain
Impact 19020049
 
Description Characterisation of ATRX function in mouse eye 
Organisation University of Ottawa
Department Ottawa Health Research Institute
Country Canada 
Sector Academic/University 
PI Contribution Provision of knockout and floxed ATRX mouse ATR-X syndrome data
Collaborator Contribution Characterisation of ATRX function in mouse eye
Impact 19088125
 
Description Characterisation of ATRX function in mouse eye 
Organisation University of Ottawa
Country Canada 
Sector Academic/University 
PI Contribution Provision of knockout and floxed ATRX mouse ATR-X syndrome data
Collaborator Contribution Characterisation of ATRX function in mouse eye
Impact 19088125
 
Description Role of ATRX in H3.3 deposition 
Organisation Rockefeller University
Department Laboratory of Chromatin Biology and Epigenetics Rockefeller
Country United States 
Sector Academic/University 
PI Contribution Supplied ATRX knockout mouse ES cells, ATRX peptides and antibodies against ATRX
Collaborator Contribution Paper in Cell: 20211137
Impact Paper in Cell: 20211137
Start Year 2007
 
Description Role of ATRX in H3.3 deposition 
Organisation Rockefeller University
Country United States 
Sector Academic/University 
PI Contribution Supplied ATRX knockout mouse ES cells, ATRX peptides and antibodies against ATRX
Collaborator Contribution Paper in Cell: 20211137
Impact Paper in Cell: 20211137
Start Year 2007
 
Description Structural analysis of the ATRX ADD domain 
Organisation Medical Research Council (MRC)
Department MRC Laboratory of Molecular Biology (LMB)
Country United Kingdom 
Sector Academic/University 
PI Contribution Determination of disease causing mutations. Design and synthesis of protein constructs.
Collaborator Contribution 1 paper 17609377
Impact 17609377
 
Description Structural analysis of the ATRX ADD domain 
Organisation Medical Research Council (MRC)
Country United Kingdom 
Sector Public 
PI Contribution Determination of disease causing mutations. Design and synthesis of protein constructs.
Collaborator Contribution Determination of structure of ATRX ADD domain and effect of disease causing mutations on this domain
Impact 17609377
 
Title NG Capture C 
Description The IP covers the Next Generation Capture-C method for massively multiplexed 3C analysis of genome interactions 
IP Reference WO2017068379 
Protection Patent application published
Year Protection Granted 2016
Licensed No
Impact None so far
 
Description 2nd Radcliffe Lecture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact XX
Year(s) Of Engagement Activity 2015
 
Description MHU Student Presentations 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact 2nd and 4th year MHU Students giving presentations on the work they are carrying out in the laboratory. These presentations will be held annually

Improve student training
Year(s) Of Engagement Activity 2013,2014,2015,2016,2017,2018,2019
 
Description Molecular Haematology Unit seminar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact A talk regarding the work on single-cell systems biology carried out by the company to date. This sparked a good debate between the presenter and the audience.
Year(s) Of Engagement Activity 2016,2017,2018,2019
 
Description Oxford Science Week 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Oxford Science week is an annual event and presentations are made to both scientists and the general public.

Considerable interest from those attending
Year(s) Of Engagement Activity 2008,2009,2010,2011,2012,2013,2014,2015
 
Description Student Presentations 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact 3rd year students present their work to the members of the Weatherall Institute of Molecular Medicine. This presentation day is held annually.

Improved student training
Year(s) Of Engagement Activity 2006,2007,2008,2009,2010,2011,2012,2013,2014,2015
 
Description Student work experience 
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 School children aged 16-18 have the opportunity to work in the lab for a period of 1 week

Some have gone on to study medicine of biomedical sciences at University
Year(s) Of Engagement Activity 2006,2007,2008,2009,2011,2012,2013,2014,2015,2016,2017,2018,2019