Reik Group | Epigenetic reprogramming

Reik Group | Epigenetic reprogramming

Reik Group


Our Research and Approach

We work on epigenetic gene regulation in mammalian development and ageing. We focus on a mechanistic and biological understanding of global epigenetic reprogramming which occurs in early embryos and in primordial germ cells to return the genome to pluripotency, erase acquired epimutations, and potentially to expose retrotransposons to be silenced. Following global erasure of epigenetic memory there is epigenetic priming in the epiblast lineage which may be uniquely associated with epigenetic and transcriptional heterogeneity, creating the potential for cell fate decision making leading up to gastrulation. In the adult organism epigenetic and transcriptional heterogeneity of tissues may change during ageing, contributing to decline of transcriptional network coherence and functional decline. We are developing new methods in single cell genomics (as part of the Sanger/EBI Single Cell Genomics Centre), particularly those in which epigenetic marks are connected with transcription networks within single cells. In collaboration with colleagues we are involved in developing new computational and modelling approaches for single cell genomics.


Reik, Wolf
Professor Wolf Reik, FRS, FMedSci
Group Leader

Wolf Reik is interested in epigenetic gene regulation in mammalian development. His current research focuses on epigenetic heterogeneity in development and ageing, making use of single cell genomics. He is a founding member of the Single Cell Genomics Centre since 2013.  

Key Projects, Collaborations, Tools & Data

Our key collaborations at Sanger are with the Single Cell Genomics Centre, particularly with the Marioni, Teichmann, Stegle, Voet, and Hemberg groups. This is focussed on methods development for single cells including new computational and modelling approaches. There are a number of projects that the Centre is involved in, including decoding cell fate decision making during gastrulation, and the development of novel tools for lineage tracing during embryogenesis, which are supported by Wellcome Trust awards. 

Programmes, Associate Research Programmes and Facilities

Partners and Funders

Internal Partners


  • Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells.

    von Meyenn F, Iurlaro M, Habibi E, Liu NQ, Salehzadeh-Yazdi A et al.

    Molecular cell 2016;62;6;848-861

  • Maternal DNA Methylation Regulates Early Trophoblast Development.

    Branco MR, King M, Perez-Garcia V, Bogutz AB, Caley M et al.

    Developmental cell 2016;36;2;152-63

  • Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity.

    Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ et al.

    Nature methods 2016;13;3;229-232

  • Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.

    Smallwood SA, Lee HJ, Angermueller C, Krueger F, Saadeh H et al.

    Nature methods 2014;11;8;817-820

  • FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency.

    Ficz G, Hore TA, Santos F, Lee HJ, Dean W et al.

    Cell stem cell 2013;13;3;351-9

  • The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells.

    Seisenberger S, Andrews S, Krueger F, Arand J, Walter J et al.

    Molecular cell 2012;48;6;849-62

  • Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution.

    Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F et al.

    Science (New York, N.Y.) 2012;336;6083;934-7

  • The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r.

    Keniry A, Oxley D, Monnier P, Kyba M, Dandolo L et al.

    Nature cell biology 2012;14;7;659-65

  • Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation.

    Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F et al.

    Nature 2011;473;7347;398-402

  • Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency.

    Popp C, Dean W, Feng S, Cokus SJ, Andrews S et al.

    Nature 2010;463;7284;1101-5

  • Tet3 regulates cellular identity and DNA methylation in neural progenitor cells.

    Santiago M, Antunes C, Guedes M, Iacovino M, Kyba M et al.

    Cellular and molecular life sciences : CMLS 2019

  • Voices in methods development.

    Anikeeva P, Boyden E, Brangwynne C, Cissé II, Fiehn O et al.

    Nature methods 2019;16;10;945-951

  • Distinct Molecular Trajectories Converge to Induce Naive Pluripotency.

    Stuart HT, Stirparo GG, Lohoff T, Bates LE, Kinoshita M et al.

    Cell stem cell 2019;25;3;388-406.e8

  • Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1.

    Martin-Herranz DE, Aref-Eshghi E, Bonder MJ, Stubbs TM, Choufani S et al.

    Genome biology 2019;20;1;146

  • TET3 prevents terminal differentiation of adult NSCs by a non-catalytic action at Snrpn.

    Montalbán-Loro R, Lozano-Ureña A, Ito M, Krueger C, Reik W et al.

    Nature communications 2019;10;1;1726

  • A single-cell molecular map of mouse gastrulation and early organogenesis.

    Pijuan-Sala B, Griffiths JA, Guibentif C, Hiscock TW, Jawaid W et al.

    Nature 2019;566;7745;490-495

  • Dppa2 and Dppa4 directly regulate the Dux-driven zygotic transcriptional program.

    Eckersley-Maslin M, Alda-Catalinas C, Blotenburg M, Kreibich E, Krueger C and Reik W

    Genes & development 2019;33;3-4;194-208

  • Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution.

    Messmer T, von Meyenn F, Savino A, Santos F, Mohammed H et al.

    Cell reports 2019;26;4;815-824.e4

  • 5-Formylcytosine organizes nucleosomes and forms Schiff base interactions with histones in mouse embryonic stem cells.

    Raiber EA, Portella G, Martínez Cuesta S, Hardisty R, Murat P et al.

    Nature chemistry 2018;10;12;1258-1266

  • Hepatic gene body hypermethylation is a shared epigenetic signature of murine longevity.

    Hahn O, Stubbs TM, Reik W, Grönke S, Beyer A and Partridge L

    PLoS genetics 2018;14;11;e1007766

  • Genome-Scale Oscillations in DNA Methylation during Exit from Pluripotency.

    Rulands S, Lee HJ, Clark SJ, Angermueller C, Smallwood SA et al.

    Cell systems 2018;7;1;63-76.e12

  • Defective germline reprogramming rewires the spermatogonial transcriptome.

    Vasiliauskaitė L, Berrens RV, Ivanova I, Carrieri C, Reik W et al.

    Nature structural & molecular biology 2018;25;5;394-404

  • Dynamics of the epigenetic landscape during the maternal-to-zygotic transition.

    Eckersley-Maslin MA, Alda-Catalinas C and Reik W

    Nature reviews. Molecular cell biology 2018

  • Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data.

    Olova N, Krueger F, Andrews S, Oxley D, Berrens RV et al.

    Genome biology 2018;19;1;33

  • Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation.

    Mohammed H, Hernando-Herraez I, Savino A, Scialdone A, Macaulay I et al.

    Cell reports 2017;20;5;1215-1228

  • Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity.

    Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ et al.

    Nature methods 2016;13;3;229-232