Role of germline transcription events in DNA methylation acquisition at imprinted genes

Lead Research Organisation: Babraham Institute
Department Name: Epigenetics

Abstract

We inherit genes from our fathers and mothers and, for most of our genes, the copies we receive from either parent are equally active. An important exception to this general rule occurs in a process called genomic imprinting, whereby one gene copy is deliberately silenced. These imprinted genes are important in determining how the fetus grows and how infants adapt their physiology to life outside the womb. But the fact that these genes have one copy that is preselected to being silent poses a risk and makes them particularly vulnerable to mutation events, such as occurs in cancer. Imprinted genes behave in this manner because they are marked in different ways in the male and female germ cells. How these genes are so marked is not fully known, and it is important to find out, because if the marking process goes wrong problems in fertility or developmental abnormalities may arise. By analysing a single imprinted gene in some detail, we have discovered an important part of the mechanism in the germ cell marking event. In this research, we wish to understand this mechanism in more detail and we need to show that it may apply generally to imprinted genes. This work will be done in a model system, but it will provide important new insights for human studies.

Technical Summary

Genomic imprinting refers to the differential epigenetic marking of genes in the male and female gametes, which results in the silencing of one of the parental alleles in somatic tissues. Imprinted genes perform essential roles in the placenta and fetus to control nutrient provision and growth, and after birth to coordinate physiological adaptations to feeding, independent metabolic control, and also mental function. In addition to the characterised imprinted syndromes, disruption of imprinting occurs widely in cancers, has been described in association with assisted reproductive technologies (ART), and imprinted genes are regarded as important potential targets in the developmental programming of chronic adult disease.
A fundamental but poorly understood mechanism in imprinting is the marking by CpG methylation of imprinting control regions (ICRs) in germ cells, particularly in the female germline, which is where the majority of imprinting is established. Although the protein factors responsible are known to be the de novo DNA methyltransferase Dnmt3a and its cofactor Dnmt3L, the key issue of how these factors select ICRs as targets for methylation is unclear. Recent work suggests involvement of the methylation state of lysine 4 on histone H3 and the patterning of CpG dinucleotides. Working in the mouse Gnas locus, we now have compelling evidence that a transcriptional event is also essential for establishment of germline methylation marks.
In this application, we shall investigate the mechanistic links between transcription and methylation establishment in oocytes. We shall examine their temporal relationship, including the development of a new knock-out in the Gnas locus in which we can delete the essential transcript at various times in germ cell development. We shall look at the histone properties of the sequences to be methylated and their dependence on transcriptional events. We shall investigate the generality of our proposed mechanism for imprinted loci, including the generation of a loss-of-imprinting allele, based on our model, of the Zac1 gene, which is implicated in the imprinted disorder 6q24 transient neonatal diabetes.
Insights gained from this work will be directly relevant to the causes of imprinted gene disorders and global errors in imprinting, and potentially to imprinting defects which may be associated with ART and other aberrant methylation events, such as tumour suppressor genes.

Publications

10 25 50

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Kelsey G (2012) Imprinted genes and the number is? in PLoS genetics

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Kelsey G (2011) A web of imprinting in stem cells. in Cell stem cell

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Kelsey G (2013) New insights into establishment and maintenance of DNA methylation imprints in mammals. in Philosophical transactions of the Royal Society of London. Series B, Biological sciences

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Kelsey G (2011) DNA methylation: a new twist in the tail. in Cell research

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Smallwood SA (2012) De novo DNA methylation: a germ cell perspective. in Trends in genetics : TIG

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Tomizawa S (2012) DNA methylation establishment during oocyte growth: mechanisms and significance. in The International journal of developmental biology

 
Description EU International Training Network
Amount £238,450 (GBP)
Funding ID PITN-GA-2011-29013 
Organisation Marie Sklodowska-Curie Actions 
Sector Charity/Non Profit
Country Global
Start 09/2012 
End 08/2016
 
Description MRC Collaborative Grant
Amount £734,199 (GBP)
Funding ID G0801156 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 10/2009 
End 09/2013
 
Description MRC Programme Grant
Amount £2,400,000 (GBP)
Funding ID MR/K011332/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 01/2013 
End 12/2017
 
Description Polish Ministry of Science and Higher Education (Mobility Plus programme)
Amount £36,000 (GBP)
Organisation Government of Poland 
Department Polish Ministry of Science and Higher Education
Sector Public
Country Poland
Start 11/2011 
End 10/2012
 
Title Oocyte CpG island methylation 
Description Genome-wide profile of CpG island methylation in mouse oocytes, sperm and blastocysts obtained next generation sequencing technique we adapted to work on very small amounts of DNA. These data have been published (Smallwood et al. 2011 Nat. Genet) and the full sequencing data made available through the Nucleotide Short Read Archive (hosted at the EBI). 
Type Of Material Biological samples 
Year Produced 2011 
Provided To Others? Yes  
Impact Impacts will result from applying the underlying method to profile human gametes/preimplantation embryos to provide a methylation reference map against which to assess the impact of assisted reproduction techniques on epigenetic profile of embryos. 
 
Title DNA methylation during mouse oogenesis 
Description Genome-wide DNA methylation datasets by RRBS and PBAT from size-selected mouse oocytes during the oocyte growth phase. Published in Gahurova et al. 2017 Epigenetics and Chromatin. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact Only recently released, impact outside of research group too early to say. 
URL https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE86297
 
Title Dynamic CpG island methylation landscape in oocytes and preimplantation embryos 
Description Sequence submitted to online database (ENA/SRA) 
Type Of Material Database/Collection of data 
Year Produced 2011 
Provided To Others? No  
Impact No actual impacts realised to date 
URL http://www.ebi.ac.uk/ena/data/view/ERP000689
 
Title Gene expression during mouse oogenesis 
Description Deeply sequenced RNA-seq datasets from size-selected mouse oocytes during the oocyte growth phase. Published in Gahurova et al. 2017 Epigenetics and Chromatin. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact Only recently released, too early to identify impacts beyond research group. 
URL https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE86297
 
Description Analysis of histone modifications in mice with loss-of-imprinting of Zac1 
Organisation Clermont Université
Country France 
Sector Academic/University 
PI Contribution Our group was responsible for framing the project and experimental design; we provided tissues from mice with loss-of-imprinting of Zac1.
Collaborator Contribution Their group performed ChIP-PCR analysis in tissues from Zac1 loss-of-imprinting mice we provided.
Impact Joint publication Veselovska et al. 2015 Genome Biol.
Start Year 2013
 
Description CpG island methylation in oocytes 
Organisation National Research Institute for Child Health and Development
Department Department of Maternal-Fetal Biology
Country Japan 
Sector Academic/University 
PI Contribution My research team developed a method to profile CpG island methylation in mouse oocytes.
Collaborator Contribution Provision of essential research material that has resulted in a joint publication
Impact Joint publication from my group: Smallwood et al., 2011 Nat. Genet. 43, 811-814.
Start Year 2009
 
Description Next generation sequencing high throughput epigenomics 
Organisation University of Cambridge
Department Department of Physiology, Development and Neuroscience
Country United Kingdom 
Sector Academic/University 
PI Contribution Part of a joint application for a MCR Collaborative Grant between the Babraham Institute (led by Prof. W. Reik) and Physiology, Development and Neurosciences, University of Cambridge, towards the establishment of a next generation sequencing capacity for epigenomics research.
Collaborator Contribution This was part of a joint application for a MRC Collaborative Grant between the Babraham Institute (led by Prof. W. Reik) and Physiology, Development and Neurosciences.
Impact My group benefitted directly from this capability from 2010.
Start Year 2009
 
Description Royal Society Exhibition, London 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Type Of Presentation Poster Presentation
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Participated in design and manning of the Epigenetics display from teh Babraham Institute during the week-long Royal Society Summer Exhibition, July 2012

Question and answer interchanges with members of the public of a wide-range of ages, interests and background.
Year(s) Of Engagement Activity 2012
 
Description TNDM Day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Type Of Presentation Keynote/Invited Speaker
Geographic Reach International
Primary Audience Participants in your research and patient groups
Results and Impact 15 patients and families of transient neonatal diabetes (TNDM)cases, as well as clinical geneticists and paediatricians involved in TNDM diagnosis, clinical management, genetic counselling and research, participating in a workshop intended to exchange information about current state of TNDM research and patient management. Event was supported by funding from the Wellcome Trust.

Opportunity to present current understanding of epigenetic errors associated with TNDM and associated genetic risk in families. Opportunity to interact with clinical geneticists who provide molecular diagnosis to exchange knowledge of possible molecular causes.
Year(s) Of Engagement Activity 2011