Characterisation of ATRX, a chromatin remodelling protein

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 the next phase of our research we wish to build on the success of the last five years to understand the role of ATRX in the gene expression and in particular how mutations in ATRX lead to down regulation of ? globin gene expression. The long term aim of this work is to see if this pathway is open to manipulation and whether it might be exploited therapeutically to modify the severity of ? thalassaemia by reducing the pathological accumulation of ? globin chains.
It is apparent from our recent work that ATRX binds to tandem repeats throughout the genome. Many of these repeats are predicted to fold into non-B forms of DNA including G4 structures and we have shown that ATRX can bind G4 in vitro. When ATRX is mutated the expression of genes close to these ATRX targets is perturbed and the magnitude of the effect is related to the size of the repeat. It seems likely that ATRX modulates the effects of these repeats on gene expression. The current conundrum is how this might occur. Preliminary evidence suggests that ATRX plays a role in DNA replication and our working hypothesis is that these repeats and the structures they form inhibit the progress of the replication fork, a DNA damage response is triggered and as a consequence of this the expression of nearby genes is perturbed. A central focus of this programme will be to test this hypothesis and understand the mechanism underlying the abnormality in gene expression seen in individuals with ATR-X syndrome.

Publications

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Chen E (2014) JAK2V617F promotes replication fork stalling with disease-restricted impairment of the intra-S checkpoint response. in Proceedings of the National Academy of Sciences of the United States of America

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Clynes D (2013) ATRX and the replication of structured DNA. in Current opinion in genetics & development

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Clynes D (2013) The chromatin remodeller ATRX: a repeat offender in human disease. in Trends in biochemical sciences

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Gibbons RJ (2012) a-Thalassemia, mental retardation, and myelodysplastic syndrome. in Cold Spring Harbor perspectives in medicine

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Hughes JR (2013) High-resolution analysis of cis-acting regulatory networks at the a-globin locus. in Philosophical transactions of the Royal Society of London. Series B, Biological sciences

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Kowalczyk MS (2012) Nprl3 is required for normal development of the cardiovascular system. in Mammalian genome : official journal of the International Mammalian Genome Society

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Kowalczyk MS (2012) Intragenic enhancers act as alternative promoters. in Molecular cell

 
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 allowing accurate and timely diagnosis; carrier testing affording affected females the information regarding their risk of having an affected child; prenatal diagnosis leading to a decease in the incidence of ATR-X syndrome.
 
Description Member of teaching faculty for Fundamentals of Clinical Genomics Course
Geographic Reach Europe 
Policy Influence Type Influenced training of practitioners or researchers
Impact This course informs the participants (predominantly consultant clinical geneticists and trainees) of the latest developments in clinical genomics
 
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 Commonwealth Scholarship
Amount £223,000 (GBP)
Organisation The Commonwealth Fund 
Sector Charity/Non Profit
Country United States
Start 10/2012 
End 09/2015
 
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 FP7 Marie Curie Network - ITN
Amount £213,151 (GBP)
Organisation Marie Sklodowska-Curie Actions 
Sector Charity/Non Profit
Country Global
Start 11/2009 
End 11/2013
 
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 Oxford Nuffield Medical Fellowship
Amount £124,000 (GBP)
Organisation Nuffield Foundation 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2012 
End 03/2017
 
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 
Provided To Others? Yes  
Impact Multiple publications 
 
Title ATRX monoclonal antibody 
Description Antibody raise in collaboration with Kevin Gatter against both isoforms of the ATRX protein 
Type Of Material Antibody 
Year Produced 2006 
Provided To Others? Yes  
Impact Many publications have resulted from the use of this reagent Now made available commercially (2017) 
 
Title Conditional knockout for ATRX gene in mouse 
Description Conditional knockout for ATRX gene in mouse 
Type Of Material Model of mechanisms or symptoms - mammalian in vivo 
Year Produced 2007 
Provided To Others? Yes  
Impact Multiple publications on the function of ATRX - latest 2 papers in 2018 
 
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 
 
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 DISCHROM 
Organisation Marie Sklodowska-Curie Actions
Country Global 
Sector Charity/Non Profit 
PI Contribution Graduate student in Initial Training Network
Collaborator Contribution Nil
Impact Nil
Start Year 2010
 
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 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 Tumours of the nervous system: from biology to therapy 
Organisation University College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Provison of ATRX Knockout and Floxed mice
Collaborator Contribution PML expertise
Impact None yet
Start Year 2014
 
Title ATRX monoclonal antibodies 
Description Development of monoclonal antibodies against ATRX 
IP Reference  
Protection Protection not required
Year Protection Granted 2015
Licensed Yes
Impact None as yet
 
Description Oxford Science week 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact ~100 individuals from the public attended the event

Great enthusiasm for the event, requests for work experience
Year(s) Of Engagement Activity Pre-2006,2012
 
Description Providing work experience placements for students (16yrs) 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Stimulates the interest of students in engaging in research

Great enthusiasm of participants
Year(s) Of Engagement Activity 2008,2009,2010,2011,2012,2013,2014,2015,2016