Single-cell analysis of the earliest cell fate decisions in development

Single-cell analysis of the earliest cell fate decisions in development

Single-cell analysis of the earliest cell fate decisions in development

Key points:

  • Uniting three different parameters in single cells taken from mouse embryos reveals more about how foundational cell identities are established in early development
  • The first single-cell multi-omics analysis of gastrulation allows researchers to connect gene expression, DNA methylation and chromatin accessibility to understand the role of the epigenome in regulating cell fate decisions in early development.
  • The findings propose how embryonic cells may be deviated away from a default cell state and awoken to new developmental possibilities during gastrulation, and plots the timeline of the epigenetic events controlling cell identity.
  • The research brings together expertise in single-cell analysis, computational methods and machine learning from the Babraham Institute, European Bioinformatics Institute, CRUK Cambridge Institute and Wellcome – MRC Cambridge Stem Cell Institute.

Researchers at the Babraham Institute, EMBL’s European Bioinformatics Institute (EMBL-EBI), CRUK Cambridge Institute and the Wellcome – MRC Cambridge Stem Cell Institute have provided the first single-cell epigenomic analysis of gastrulation, a crucial process in early embryo development. The researchers analysed over 1,000 cells from mouse embryos to understand the epigenetic priming events preceding gastrulation and the cell fate decisions these establish. The findings, published today (Wednesday) in Nature, uncover fundamental knowledge about the processes that programme cell fate in the early embryo to generate all the organs and tissues of the body.

Just as with the construction of a building, one of the first steps before creating the upright structure is to set the foundations and the floorplan. Mammalian development is not so different. The gastrulation process takes the embryo from a ball of largely undifferentiated cells and establishes the head-to-tail and front-to-back axes and three foundational cellular layers that are each responsible for creating specific parts of the embryo.

The three layers (called germ layers) established during gastrulation are the ectoderm, mesoderm and endoderm. The ectoderm gives rise to the skin and the nervous system, the mesoderm specifies the development of several cell types such as bone, muscle and connective tissue, and cells in the endoderm layer subsequently become the linings of the digestive and respiratory system, and form organs such as the liver and the pancreas.

Building on exciting progress in the use of cutting-edge single-cell and computational techniques to understand early development, the researchers used two pioneering methods to collect and analyse the gastrulation data. The first was a technique developed at the Babraham Institute called scNMT-seq (single-cell Nucleosome, Methylome and Transcriptome sequencing). This was used to obtain multiple biological read-outs from 1,105 single cells taken from mouse embryos at different development stages spanning the gastrulation process. In each cell, the researchers assessed gene expression activity, DNA methylation and chromatin accessibility to chart how these changed as cells went through the gastrulation process.

The second was a computational method developed by researchers at EMBL-EBI called Multi-Omics factor Analysis (MOFA). This machine-learning approach, originally developed for personalised medicine, allowed the researchers to unite the three streams of biological information profiled from each single cell.

Ricard Argelaguet, a PhD student at the EMBL-EBI co-supervised by John Marioni and Oliver Stegle, said “MOFA offers a principled approach for combining high-dimensional multi-omics data. It helped us to identify the elements in the genome that are associated with cell fate commitment as well as enabling us to understand how different molecular features interact with one another throughout gastrulation.”

The researchers found that the three germ layers (ectoderm, mesoderm and endoderm) showed differences in the timing of epigenetic events in a hierarchical way. The analysis demonstrated that ectoderm cells were primed epigenetically at an earlier developmental stage. This finding may explain the existence of a pre-programmed default developmental path specifying skin and brain identities. Epigenetic events occurring later in mesoderm and endoderm cells may act to actively divert these cells away from this default path by making the cells receptive to signals promoting other cell identities.

“Through analysing the timeline of events, we identified that the diversification of the three gastrulation layers was mainly driven by epigenetic events affecting germ layer specific enhancers.” said Dr Stephen Clark, lead researcher and one of the paper’s four joint first authors. “We found that the epigenome of the ectoderm layer was established much earlier in development than the other two, even though all three cell types arise at a similar time.”

Professor Wolf Reik, Head of the Epigenetics Programme at the Babraham Institute, said “This is the first comprehensive application of the single-cell method developed here at the Institute to a biological question and gives a new view on how cell fate is established. Our findings develop our understanding of the role of the epigenome in defining cell fate commitments at different stages of development, with important implications for stem cell biology and medicine. It is very enjoyable to see how the multidisciplinary research community that has come together in this project is now sharing the success of their efforts.”

Dr John Marioni, Group Leader at the EMBL-EBI and the CRUK Cambridge Institute, said “The ability of a cell to commit to a specific fate requires integration of a complex array of different molecular signals. Analogously, understanding this process requires combining cutting-edge experimental and computational tools, as exemplified in this work. Importantly, our data and analyses provide a blueprint for how the epigenome might regulate cell fate choice in other contexts, providing an exciting launch pad for future studies.”

A newly announced research initiative, the Wellcome-funded Human Developmental Biology Initiative, will utilise the same single-cell methods to analyse cells from human embryos. The initiative, which involves several of the paper’s authors (Professor Wolf Reik, Dr Gavin Kelsey, Dr Peter Rugg-Gunn, each a group leader at the Babraham Institute, and Professor Bertie Göttgens, Principal Investigator, Wellcome – MRC Cambridge Stem Cell Institute) might provide insight as to whether the same epigenetic mechanisms of control work similarly in humans.

Single-cell multi-omics analysis is also likely to deliver significant impacts for human healthcare in future years. A pan-European research initiative, LifeTime, is bringing together life science experts with leaders in the pharma, clinical medicine and technology industries to map how innovation and cutting-edge technologies (including single-cell multi-omics methods) can be united to revolutionise healthcare.  


Notes to Editors

Publication reference

Argelaguet, Clark, Mohammed, Stapel et al. Multi-omics profiling of mouse gastrulation at single-cell resolution. Nature. DOI: 10.1038/s41586-019-1825-8

Press contact

Dr Louisa Wood, Babraham Institute Communications Manager,, 01223 496230

Research funding

This work was supported by funding from the Wellcome Trust jointly awarded to Wolf Reik, Jennifer Nichols, Berthold Gottgens and John Marioni. The Epigenetics research programme at the Babraham Institute is core funded by an Institute Strategic Programme grant from the UKRI Biotechnology and Biological Sciences Research Council. Carine Stapel is a Marie Skłodowska-Curie fellow. In addition, the study received financial support from EMBL, Cancer Research UK and the UKRI Medical Research Council.

Image description:

The image shows that, for each single cell across four developmental time points (4.5 -7.5 days after fertilisation (E4.5 to E7.5)), we obtain three separate molecular profiles: chromatin accessibility, DNA methylation and RNA expression. The embryo and cell images were created by Veronique Juvin from SciArtWork. Data plots were produced by Ricard Argelaguet, EMBL-EBI.

Affiliated authors (in author order):

Stephen Clark (joint first author) - senior research scientist, Reik lab
Hisham Mohammed (joint first author) - former postdoc, Reik lab
Carine Stapel (joint first author) - Marie Skłodowska-Curie fellow, Reik lab
Christel Krueger - Bioinformatician, Bioinformatics group
Courtney Hanna - Former postdoc in the Kelsey lab, currently a Next Generation Fellow, Centre of Trophoblast Research
Felix Krueger - Bioinformatician, Bioinformatics group
Peter Rugg-Gunn - group leader, Epigenetics research programme
Gavin Kelsey - group leader, Epigenetics research programme
Wendy Dean – former senior research scientist, Reik lab
Wolf Reik, Head of Epigenetics research programme


Additional/related resources:

EMBl-EBI news article: Using multiomics to define the mammalian primary germ layers, 11th December 2019
News: Senior researcher Stephen Clark named Researcher of the Year, 6th November 2019
News: Human Developmental Biology Initiative announced, 25th July 2019
Wellcome Trust: Initiative brings biologists together to crack the secrets of early development. Opinion article 25th July 2019
News: Establishing the molecular blueprint of early embryo development, 20th February 2019
News: New technique offers insights into early life 22 February 2018
Research feature: Unlocking the secrets of early development, Annual Research Report 2016 (view report)
Press release: New method allows study of DNA methylation and gene expression in the same cell 11 January 2016

Animal research statement:

As a publicly funded research institute, the Babraham Institute is committed to engagement and transparency in all aspects of its research. The research presented here used mice to create embryos which were collected from pregnant mice at specific developmental stages. All mouse experimentation was approved by the Babraham Institute Animal Welfare and Ethical Review Body. Animal husbandry and experimentation complied with existing European Union and United Kingdom Home Office legislation.

Please follow the link for further details of our animal research and our animal welfare practices.

About the Babraham Institute

The Babraham Institute undertakes world-class life sciences research to generate new knowledge of biological mechanisms underpinning ageing, development and the maintenance of health. Our research focuses on cellular signalling, gene regulation and the impact of epigenetic regulation at different stages of life. By determining how the body reacts to dietary and environmental stimuli and manages microbial and viral interactions, we aim to improve wellbeing and support healthier ageing. The Institute is strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation, through an Institute Core Capability Grant and also receives funding from other UK research councils, charitable foundations, the EU and medical charities.

About the European Bioinformatics Institute

EMBL’s European Bioinformatics Institute (EMBL-EBI) is a global leader in the storage, analysis and dissemination of large biological datasets. We help scientists realise the potential of ‘big data’ by enhancing their ability to exploit complex information to make discoveries that benefit humankind. We are at the forefront of computational biology research, with work spanning sequence analysis methods, multi-dimensional statistical analysis and data-driven biological discovery, from plant biology to mammalian development and disease. We are part of EMBL and are located on the Wellcome Genome Campus, one of the world’s largest concentrations of scientific and technical expertise in genomics.

About the Wellcome - MRC Cambridge Stem Cell Institute

The Wellcome - MRC Cambridge Stem Cell Institute is a world-leading centre for stem cell research with a mission to transform human health through a deep understanding of normal and pathological stem cell behaviour. Bringing together biological, clinical and physical scientists operating across a range of tissue types and at multiple scales, we explore the commonalities and differences in stem cell biology in a cohesive and inter-disciplinary manner. In 2019, the institute relocated to a new purpose-built home on the Cambridge Biomedical Campus. Housing over 350 researchers, including a critical mass of clinician scientists, the Institute integrates with neighbouring disease-focused research institutes and also acts as a hub for the wider stem cell community in Cambridge.

About the Cancer Research UK Cambridge Institute

The Cancer Research UK Cambridge Institute combines basic and clinical research with innovative technologies to address key questions in the diagnosis and treatment of cancer. As one of the largest cancer research facilities in Europe, we provide an unrivalled biomedical research environment, bringing together the world-class science of the University of Cambridge with clinical and industrial partners at the Cambridge Biomedical Campus. Our research focuses on tumour ecology and evolution, ranging from basic experimental and computational biology through translational cancer research to clinical application.