Abstract

We report scM&T-seq, a method for parallel single-cell genome-wide methylome and transcriptome sequencing that allows for the discovery of associations between transcriptional and epigenetic variation. Profiling of 61 mouse embryonic stem cells confirmed known links between DNA methylation and transcription. Notably, the method revealed previously unrecognized associations between heterogeneously methylated distal regulatory elements and transcription of key pluripotency genes.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

Primary accessions

Gene Expression Omnibus

Referenced accessions

Gene Expression Omnibus

Data deposits

This study reused some data from Smallwood et al.3 available in the Gene Expression Omnibus under accession GSE56879.

References

  1. 1.

    , & Nat. Rev. Genet. 14, 618–630 (2013).

  2. 2.

    et al. Genome Res. 23, 2126–2135 (2013).

  3. 3.

    et al. Nat. Methods 11, 817–820 (2014).

  4. 4.

    et al. Cell Rep. 10, 1386–1397 (2015).

  5. 5.

    , , & Science 297, 836–840 (2002).

  6. 6.

    et al. Nat. Struct. Mol. Biol. 20, 1131–1139 (2013).

  7. 7.

    et al. Nat. Methods 12, 519–522 (2015).

  8. 8.

    , , , & Nat. Biotechnol. 33, 285–289 (2015).

  9. 9.

    Nature 517, 321–326 (2015).

  10. 10.

    Nat. Rev. Genet. 13, 484–492 (2012).

  11. 11.

    et al. Mol. Cell 55, 319–331 (2014).

  12. 12.

    et al. PLoS Biol. 7, e1000149 (2009).

  13. 13.

    et al. Nature 450, 1230–1234 (2007).

  14. 14.

    , , & Stem Cells 25, 2534–2542 (2007).

  15. 15.

    & Development 141, 2173–2181 (2014).

  16. 16.

    et al. Cell Stem Cell 13, 351–359 (2013).

  17. 17.

    et al. Cell 161, 1187–1201 (2015).

  18. 18.

    et al. Cell Stem Cell 17, 471–485 (2015).

  19. 19.

    et al. Cell Stem Cell 13, 360–369 (2013).

  20. 20.

    et al. Nature 480, 490–495 (2011).

  21. 21.

    , & Cell Stem Cell 14, 710–719 (2014).

  22. 22.

    & EMBO J. 31, 4255–4257 (2012).

  23. 23.

    et al. Cell 153, 307–319 (2013).

  24. 24.

    & Bioinformatics 27, 1571–1572 (2011).

  25. 25.

    & Bioinformatics 26, 873–881 (2010).

  26. 26.

    , & Genome Biol. 15, 550 (2014).

  27. 27.

    et al. Nat. Biotechnol. 28, 511–515 (2010).

  28. 28.

    , & Proc. Natl. Acad. Sci. USA 107, 9546–9551 (2010).

Download references

Acknowledgements

We thank A. Kolodziejczyk and S.A. Teichmann for providing a list of 86 ESC pluripotency and differentiation genes18. We thank W. Haerty for his supervision and valuable advice to T.X.H. We thank the Wellcome Trust Sanger Institute sequencing pipeline team for assistance with Illumina sequencing. We thank the members of the Sanger–European Bioinformatics Institute (EBI) Single-Cell Genomics Centre for general advice. W.R. is supported by the UK Biotechnology and Biological Sciences Research Council (BBSRC), the Wellcome Trust and the EU. G.K. is supported by the BBSRC, the UK Medical Research Council (MRC) and the EU. C.P.P. is supported by the Wellcome Trust and the MRC. T.V. is supported by the Wellcome Trust and KU Leuven (SymBioSys, PFV/10/016). H.J.L. is supported by EU Network of Excellence EpiGeneSys. O.S. is supported by the European Molecular Biology Laboratory (EMBL), the Wellcome Trust and the EU.

Author information

Author notes

    • Christof Angermueller
    • , Stephen J Clark
    • , Heather J Lee
    •  & Iain C Macaulay

    These authors contributed equally to this work.

Affiliations

  1. European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.

    • Christof Angermueller
    • , Tim Xiaoming Hu
    •  & Oliver Stegle
  2. Epigenetics Programme, Babraham Institute, Cambridge, UK.

    • Stephen J Clark
    • , Heather J Lee
    • , Sébastien A Smallwood
    • , Gavin Kelsey
    •  & Wolf Reik
  3. Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

    • Heather J Lee
    • , Iain C Macaulay
    • , Mabel J Teng
    • , Tim Xiaoming Hu
    • , Chris P Ponting
    • , Thierry Voet
    •  & Wolf Reik
  4. Medical Research Council Functional Genomics Unit, University of Oxford, Oxford, UK.

    • Tim Xiaoming Hu
    •  & Chris P Ponting
  5. Bioinformatics Group, Babraham Institute, Cambridge, UK.

    • Felix Krueger
  6. Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium.

    • Thierry Voet

Authors

  1. Search for Christof Angermueller in:

  2. Search for Stephen J Clark in:

  3. Search for Heather J Lee in:

  4. Search for Iain C Macaulay in:

  5. Search for Mabel J Teng in:

  6. Search for Tim Xiaoming Hu in:

  7. Search for Felix Krueger in:

  8. Search for Sébastien A Smallwood in:

  9. Search for Chris P Ponting in:

  10. Search for Thierry Voet in:

  11. Search for Gavin Kelsey in:

  12. Search for Oliver Stegle in:

  13. Search for Wolf Reik in:

Contributions

C.A. performed all statistical analyses of the data. H.J.L., I.C.M., S.J.C. and S.A.S. developed the protocol and performed experiments. H.J.L., I.C.M., C.A., S.J.C., O.S., W.R. and C.P.P. interpreted the results. M.J.T. contributed to method development. T.X.H. processed RNA-seq data. F.K. processed BS-seq data. W.R., G.K., I.C.M. and T.V. contributed protocols and reagents. H.J.L., I.C.M., W.R. and T.V. conceived the project. W.R., O.S., T.V. and G.K. jointly supervised the project. O.S., H.J.L., S.J.C., W.R. and I.C.M. wrote the paper with input from all other authors. Names of authors who contributed equally to this work are ordered alphabetically on the first page.

Competing interests

W.R. is a consultant and shareholder of Cambridge Epigenetix.

Corresponding authors

Correspondence to Thierry Voet or Gavin Kelsey or Oliver Stegle or Wolf Reik.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–15 and Supplementary Table 3

Excel files

  1. 1.

    Supplementary Table 1

    scRNA-seq and scBS-seq quality metrics.

  2. 2.

    Supplementary Table 2

    Genomic contexts considered for the methylation–gene expression association analyses.

  3. 3.

    Supplementary Table 4

    Gene-level results of the association tests between DNA-methylation variation in alternative genomic contexts and gene expression variation.

  4. 4.

    Supplementary Table 5

    List of 86 literature-derived pluripotency genes.

  5. 5.

    Supplementary Table 6

    Summary statistics obtained for the cell-specific association analysis correlating the methylome and the transcriptome in individual cells.

Zip files

  1. 1.

    Supplementary Software

    scMT-seq software

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nmeth.3728

Further reading