Epigenome patterning in oocytes and its legacies in the embryo

Lead Research Organisation: Babraham Institute
Department Name: Epigenetics

Abstract

Although we inherit 22 chromosomes from each of our parents, the egg and the sperm pass on more than the bare DNA sequence. The DNA sequence and the chromosomes themselves are modified by numerous chemical tags - call epigenetic marks - that are vital for specifying which genes should be active and which silent in any cell in our body. Where these epigenetic marks are placed on the DNA is constantly being modified as cells develop and differentiate into different tissues. It is also crucial that most epigenetic marks that were present in the egg and sperm are removed at fertilisation, so that the programme of gene expression for development of the embryo can be kick started correctly. However, some epigenetic tags can persist throughout our lifetimes, and some even remain as a permanent memory of whether a gene came from the egg or sperm. As a result of this special class of tags, some genes exhibit different activities of the copy inherited from mothers and the copy from fathers. These are referred to as "imprinted genes", because they are imprinted differently in the sperm and egg. Imprinted genes are particularly important for the normal development of the placenta and for how the fetus grows.

We are trying to understand how imprinted genes are epigenetically tagged during the development of egg cells and how these tags are remembered as the embryo develops. It seems that different types of epigenetic tags are involved - some directly on DNA, some on the chromosome structure - and some marks will end up more important in the embryo itself whereas others will be more influential in the placenta, which nonetheless can control how the baby grows and develops.

Much of the work we propose will be conducted in mouse models, where we can modify the epigenetic marks on genes, or the activity of genes, and we can access tissues - egg cells and very early embryos - in a way that we cannot do so with human samples.

Some of our work uses very sensitive techniques we have developed that can read all the epigenetic marks in individual cells. We are now using these techniques to understand if there is variation in epigenetic marks in human embryos before they implant. We believe that some differences can be traced back to the eggs from which the embryos developed, leading us to propose that some epigenetic changes could be diagnostic for problems in fertility.

Technical Summary

Transmission of epigenetic information from parent to offspring is generally precluded by multiple genome-wide reprogramming steps that occur from the specification of germ cells, during gametogenesis, in the preimplantation embryo, and with establishment of lineage-specific epigenomes from implantation. Yet the extent to which there is inter-generational transmission of epigenetic states is still unclear and of substantial interest, eg, in relation to factors such as the increase in maternal obesity and the programming of adverse metabolic outcomes in offspring, or whether epigenetic fidelity is compromised by procedures for assisted reproduction. Genomic imprinting provides the best paradigm for epigenetic inheritance, and which is fundamentally important for normal offspring growth, development and long-term health. Until recently, it appeared that there was a single modality of imprinting, determined by gamete-derived DNA methylation, but recent studies prompt us to develop a more nuanced view and to recognise additional pathways to imprinting, such as chromatin-determined imprinting.

This programme will explore transcriptional control and how transcription patterns the epigenome in the oocyte and the legacies of these events in the embryo. It will investigate how DNA methylation-dependent and chromatin-dependent modes or imprinting are set up at different times in the female germline and how they contribute in different ways to developmental processes in the embryo and extra-embryonic lineages. It will assess general principles at the genome-wide scale, but also work at the level of specific loci to test mechanistic details and functional impacts of the different modes of imprinting. It will explore variation in DNA methylation in human preimplantation embryos, how this variation can be traced back to methylation variation in oocytes and seek to eludiate the genetic basis and pathophysiological correlates of such variation.

Planned Impact

Our research aims to understand fundamental processes in oocytes (egg cells) by which epigenetic information is set up, and how epigenetic information is then passed on and modified in the embryo. Epigenetic information comprises the chemical tags on the DNA or the chromosomes that help demarcate active and inactive genes. In general, epigenetic information present in oocytes is erased in the early embryo to enable the embryonic gene expression programme to be properly executed, as well as to prevent transmission of epigenetic abnormalities between parents and offspring, which could be acquired as a result of environmental factors or diet. Despite the general reprogramming of epigenetic informaion, some needs to be transmitted from the egg and faithfully maintained for proper development of the fetus; this occurs at a class of genes called imprinted genes. Recent work has shown that there is an unexpected diversity of imprinted genes specified by different types of epigenetic information present in eggs: those controlled by chemical tags directly on the DNA (methylation); or those controlled by modifications on chromosome proteins (histones). We are only beginning to understand the extent and significance for normal development of these newly identified forms of imprinting. Moreover, it is still not fully understood the extent to which epigenetic information is destabilised by environmental factors or by processes associated with assisted reproduction technologies (ART). Therefore, it is imperative that further developments in ART methods that seek to improve fertility treatments are evaluated for epigenetic safety, because epigenetic errors in early development can have long-term impacts on offspring health and modify an individual's risk of disease in later life.

Much of our research will be done in a model organism, the mouse, in which these processes are most easy to investigate and because the processes are generally conserved with human. We shall also investigate the extent of epigenetic variation in human eggs and early embryos, where we believe that DNA methylation variation could be a robust molecular marker of gene expression anomalies in the ovary, and could influence the potential of the embryo for normal development.

Therefore, we expect to have impact in knowledge of the basic molecular mechanisms that govern how genes are controlled in the egg, and in the mechanisms that determine how epigenetic information is retained in the embryo to ensure correct imprinting. These advances will have wide-ranging impact in the academic community interested in mammalian developmental epigenetics and transgenerational inheritance. And they could have impact on our understanding of possible epigenetic contributions to chronic disease for which genetic causes remain ill-defined.

Our investigation of the extent and consequences of epigenetic variation in human eggs and embryos will have impact for clinicians working in reproductive medicine and for patients seeking fertility treatments, or undergoing fertility preservation.

We also expect major impact of our research in the technical capabilities we have and the advances we shall continue to make in methods for profiling epigenetic marks in very small numbers of cells or in single cells. Such advances are having widespread application in biomedical research, providing new levels of understanding of cell-fate decisions, and cell identity and function, both in normal development and physiology and in disease. We collaborate with several groups (both academic and biotech sectors) from research areas unrelated to our field who have an interest in applying these cutting-edge methods to their own biomedical questions. Therefore, we anticipate significant impact in training and knowledge exchange also at a technical level.
 
Description European Oocyte Biology Research Innovation Training Network
Amount € 3,978,647 (EUR)
Funding ID 860960 
Organisation European Commission H2020 
Sector Public
Country Belgium
Start 11/2019 
End 10/2023
 
Title Epigenomic analysis of mouse post-implantation embryos 
Description Allellic DNA methylation, gene expression and histone modification datasets from embryonic tissues from mouse. Allows genome-wide identification of genes controlled by genomic imprinting, and distinction of imprinting conferred by DNA methylation or repressive chromatin in oocytes. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Published in Hanna et al. Genome Biol 2019 PMID: 31665063 
URL http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE124216
 
Title Methylation analysis of hydatidiform mole tissue with KHDC3L mutation 
Description DNA methylation datasets from control placenta, biparental mole with KHDC3L mutation, and sporadic androgenetic mole analysed using using Infinium MethylationEPIC 850K Bead Chip. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Published in Demond et al. Genome Med 2019 PMID: 31847873 
URL http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE138864
 
Title Methylation analysis of oocytes and embryo with KHDC3L mutation 
Description Whole-genome DNA methylation datasets from 5 oocytes and 1 preimplantation embryo from patient with a KHDC3L mutation that causes reproductive failure. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Published in Demond et al. Genome Med 2019 PMID: 31847873. Provides first evidence that mutations in components of the subcortical maternal complex of the oocyte cause a genome-wide disruption of DNA methylation establishment in oocytes that will manifest as defective imprinting in the conceptus. 
URL http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122872
 
Description Investigating role of LTRs in imprinted gene regulation 
Organisation Curie Institute Paris (Institut Curie)
Country France 
Sector Academic/University 
PI Contribution Molecular analysis of mouse embryos with deletion of LTR element controlling imprinted gene.
Collaborator Contribution Generation of mouse embryos with deletion of LTR element controlling imprinted gene.
Impact Joint publication Hanna et al. 2019 Genome Biol. PMID: 31665063
Start Year 2019
 
Description Methylation analysis of KHDC3L mutation 
Organisation National Research Council
Department Institute of Genetics and Biophysics (IGB)
Country Italy 
Sector Public 
PI Contribution Generation of methylation datasets from oocytes and preimplantation embryo and bioinformatic analysis
Collaborator Contribution Generation of methylation array datasets from placenta and molar tissue
Impact Joint publication Demond et al. Genome Med 2019 PMID: 31847873
Start Year 2019
 
Description Single-cell epigenomic profiling of spermatogonial stem cells 
Organisation Yokohama City University
Country Japan 
Sector Academic/University 
PI Contribution Our group is providing expertise in single-cell methylation and expression profiling methods.
Collaborator Contribution Their group is responsible for framing the project and experimental design and for providing isolated mouse spermatogonial stem cells.
Impact Hosted visit by post-doc from collaborating group to initiate single cell methylation/transcription profiling. Joint grant awarded: Royal Society International Exchange Award IEC\R3\170052 (March 2018 March 2020): Analysis of spermatogonial stem cell maintenance and differentiation system by the state-of-the-art single-cell technology.
Start Year 2016
 
Description Babraham Schools' Day 
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 As part of the wider Babraham Institute Schools' Day, my group ran projects for groups of 3-4 GCSE and A level students.
Year(s) Of Engagement Activity 2020
 
Description Royal Society of Medicine CPD meeting on 'Epigenetics' 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Continuing professional development event held by the Royal Society of Medicine to raise awareness of epigenetics amongst medical professionals, students, junior doctors.
Year(s) Of Engagement Activity 2019
URL https://www.rsm.ac.uk/events/medical-genetics/2018-19/mgm03/