Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Transcription factor EBF1 is essential for the maintenance of B cell identity and prevention of alternative fates in committed cells

Nature Immunology volume 14, pages 867–875 (2013)Cite this article

Subjects

Abstract

The transcription factors EBF1 and Pax5 have been linked to activation of the B cell lineage program and irreversible loss of alternative lineage potential (commitment), respectively. Here we conditionally deleted Ebf1 in committed pro-B cells after transfer into alymphoid mice. We found that those cells converted into innate lymphoid cells (ILCs) and T cells with variable-diversity-joining (VDJ) rearrangements of loci encoding both B cell and T cell antigen receptors. As intermediates in lineage conversion, Ebf1-deficient CD19+ cells expressing Pax5 and transcriptional regulators of the ILC and T cell fates were detectable. In particular, genes encoding the transcription factors Id2 and TCF-1 were bound and repressed by EBF1. Thus, both EBF1 and Pax5 are required for B lineage commitment by repressing distinct and common determinants of alternative cell fates.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Adoptive transfer of Ebf1-deficient late pro-B cells into irradiated Rag2−/−Il2rg−/− recipients leads to in vivo reconstitution of thymic T cell development.
Figure 2: Detection of lineage-converted T cells in the periphery.
Figure 3: B cell– and T cell–specific rearrangements of antigen receptor genes.
Figure 4: Conversion of 4-OHT-treated Ebf1fl/fl pro-B cells into functional ILCs in vivo.
Figure 5: Ebf1fl/fl pro-B cells treated with 4-OHT gain lineage plasticity via dedifferentiation through a CD19+ stage in vivo.
Figure 6: EBF1 and Pax5 differently regulate genes encoding molecules involved in the B cell–versus–T cell lineage identity.

Similar content being viewed by others

Accession codes

Primary accessions

Gene Expression Omnibus

Referenced accessions

Gene Expression Omnibus

References

  1. Adolfsson, J. et al. Identification of Flt3+ lympho-myeloid stem cells lacking erythro-megakaryocytic potential a revised road map for adult blood lineage commitment. Cell 121, 295–306 (2005).

    CAS  PubMed  Google Scholar 

  2. Mercer, E.M. et al. Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic progenitors. Immunity 35, 413–425 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Ng, S.Y., Yoshida, T., Zhang, J. & Georgopoulos, K. Genome-wide lineage-specific transcriptional networks underscore Ikaros-dependent lymphoid priming in hematopoietic stem cells. Immunity 30, 493–507 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Ichii, M. et al. Functional diversity of stem and progenitor cells with B-lymphopoietic potential. Immunol. Rev. 237, 10–21 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Klose, C.S., Hoyler, T., Kiss, E.A., Tanriver, Y. & Diefenbach, A. Transcriptional control of innate lymphocyte fate decisions. Curr. Opin. Immunol. 24, 290–296 (2012).

    CAS  PubMed  Google Scholar 

  6. Igarashi, H., Gregory, S.C., Yokota, T., Sakaguchi, N. & Kincade, P.W. Transcription from the RAG1 locus marks the earliest lymphocyte progenitors in bone marrow. Immunity 17, 117–130 (2002).

    CAS  PubMed  Google Scholar 

  7. Inlay, M.A. et al. Ly6d marks the earliest stage of B-cell specification and identifies the branchpoint between B-cell and T-cell development. Genes Dev. 23, 2376–2381 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Mansson, R. et al. Single-cell analysis of the common lymphoid progenitor compartment reveals functional and molecular heterogeneity. Blood 115, 2601–2609 (2010).

    CAS  PubMed  Google Scholar 

  9. Lin, Y.C. et al. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat. Immunol. 11, 635–643 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Mandel, E.M. & Grosschedl, R. Transcription control of early B cell differentiation. Curr. Opin. Immunol. 22, 161–167 (2010).

    CAS  PubMed  Google Scholar 

  11. Mansson, R. et al. Positive intergenic feedback circuitry, involving EBF1 and FOXO1, orchestrates B-cell fate. Proc. Natl. Acad. Sci. USA 109, 21028–21033 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Medina, K.L. et al. Assembling a gene regulatory network for specification of the B cell fate. Dev. Cell 7, 607–617 (2004).

    CAS  PubMed  Google Scholar 

  13. Reynaud, D. et al. Regulation of B cell fate commitment and immunoglobulin heavy-chain gene rearrangements by Ikaros. Nat. Immunol. 9, 927–936 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Seet, C.S., Brumbaugh, R.L. & Kee, B.L. Early B cell factor promotes B lymphopoiesis with reduced interleukin 7 responsiveness in the absence of E2A. J. Exp. Med. 199, 1689–1700 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Zandi, S. et al. Single-cell analysis of early B-lymphocyte development suggests independent regulation of lineage specification and commitment in vivo. Proc. Natl. Acad. Sci. USA 109, 15871–15876 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Cobaleda, C. & Busslinger, M. Developmental plasticity of lymphocytes. Curr. Opin. Immunol. 20, 139–148 (2008).

    CAS  PubMed  Google Scholar 

  17. Nutt, S.L. & Kee, B.L. The transcriptional regulation of B cell lineage commitment. Immunity 26, 715–725 (2007).

    CAS  PubMed  Google Scholar 

  18. Rothenberg, E.V. T cell lineage commitment: identity and renunciation. J. Immunol. 186, 6649–6655 (2011).

    CAS  PubMed  Google Scholar 

  19. Welinder, E., Ahsberg, J. & Sigvardsson, M. B-lymphocyte commitment: identifying the point of no return. Semin. Immunol. 23, 335–340 (2011).

    CAS  PubMed  Google Scholar 

  20. Mikkola, I., Heavey, B., Horcher, M. & Busslinger, M. Reversion of B cell commitment upon loss of Pax5 expression. Science 297, 110–113 (2002).

    CAS  PubMed  Google Scholar 

  21. Nutt, S.L., Heavey, B., Rolink, A.G. & Busslinger, M. Commitment to the B-lymphoid lineage depends on the transcription factor Pax5. Nature 401, 556–562 (1999).

    CAS  PubMed  Google Scholar 

  22. Rolink, A.G., Nutt, S.L., Melchers, F. & Busslinger, M. Long-term in vivo reconstitution of T-cell development by Pax5-deficient B-cell progenitors. Nature 401, 603–606 (1999).

    CAS  PubMed  Google Scholar 

  23. Cobaleda, C., Jochum, W. & Busslinger, M. Conversion of mature B cells into T cells by dedifferentiation to uncommitted progenitors. Nature 449, 473–477 (2007).

    CAS  PubMed  Google Scholar 

  24. Delogu, A. et al. Gene repression by Pax5 in B cells is essential for blood cell homeostasis and is reversed in plasma cells. Immunity 24, 269–281 (2006).

    CAS  PubMed  Google Scholar 

  25. McManus, S. et al. The transcription factor Pax5 regulates its target genes by recruiting chromatin-modifying proteins in committed B cells. EMBO J. 30, 2388–2404 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Decker, T. et al. Stepwise activation of enhancer and promoter regions of the B cell commitment gene Pax5 in early lymphopoiesis. Immunity 30, 508–520 (2009).

    CAS  PubMed  Google Scholar 

  27. Roessler, S. et al. Distinct promoters mediate the regulation of Ebf1 gene expression by interleukin-7 and Pax5. Mol. Cell Biol. 27, 579–594 (2007).

    CAS  PubMed  Google Scholar 

  28. Pongubala, J.M. et al. Transcription factor EBF restricts alternative lineage options and promotes B cell fate commitment independently of Pax5. Nat. Immunol. 9, 203–215 (2008).

    CAS  PubMed  Google Scholar 

  29. Thal, M.A. et al. Ebf1-mediated down-regulation of Id2 and Id3 is essential for specification of the B cell lineage. Proc. Natl. Acad. Sci. USA 106, 552–557 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Treiber, T. et al. Early B cell factor 1 regulates B cell gene networks by activation, repression, and transcription-independent poising of chromatin. Immunity 32, 714–725 (2010).

    CAS  PubMed  Google Scholar 

  31. Lukin, K. et al. A dose-dependent role for EBF1 in repressing non-B-cell-specific genes. Eur. J. Immunol. 41, 1787–1793 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Györy, I. et al. Transcription factor Ebf1 regulates differentiation stage-specific signaling, proliferation, and survival of B cells. Genes Dev. 26, 668–682 (2012).

    PubMed  PubMed Central  Google Scholar 

  33. Vilagos, B. et al. Essential role of EBF1 in the generation and function of distinct mature B cell types. J. Exp. Med. 209, 775–792 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Fuxa, M. et al. Pax5 induces V-to-DJ rearrangements and locus contraction of the immunoglobulin heavy-chain gene. Genes Dev. 18, 411–422 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Spits, H. et al. Innate lymphoid cells - a proposal for uniform nomenclature. Nat. Rev. Immunol. 13, 145–149 (2013).

    CAS  PubMed  Google Scholar 

  36. Heng, T.S. & Painter, M.W. The Immunological Genome Project: networks of gene expression in immune cells. Nat. Immunol. 9, 1091–1094 (2008).

    CAS  PubMed  Google Scholar 

  37. Dengler, H.S. et al. Distinct functions for the transcription factor Foxo1 at various stages of B cell differentiation. Nat. Immunol. 9, 1388–1398 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Kieslinger, M., Hiechinger, S., Dobreva, G., Consalez, G.G. & Grosschedl, R. Early B cell factor 2 regulates hematopoietic stem cell homeostasis in a cell-nonautonomous manner. Cell Stem Cell 7, 496–507 (2010).

    CAS  PubMed  Google Scholar 

  39. Bussmann, L.H. et al. A robust and highly efficient immune cell reprogramming system. Cell Stem Cell 5, 554–566 (2009).

    CAS  PubMed  Google Scholar 

  40. Di Tullio, A. et al. CCAAT/enhancer binding protein alpha (C/EBPα)-induced transdifferentiation of pre-B cells into macrophages involves no overt retrodifferentiation. Proc. Natl. Acad. Sci. USA 108, 17016–17021 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Germar, K. et al. T-cell factor 1 is a gatekeeper for T-cell specification in response to Notch signaling. Proc. Natl. Acad. Sci. USA 108, 20060–20065 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Weber, B.N. et al. A critical role for TCF-1 in T-lineage specification and differentiation. Nature 476, 63–68 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. García-Ojeda, M.E. et al. GATA-3 promotes T-cell specification by repressing B-cell potential in pro-T cells in mice. Blood 121, 1749–1759 (2013).

    PubMed  Google Scholar 

  44. Hoyler, T. et al. The transcription factor GATA-3 controls cell fate and maintenance of type 2 innate lymphoid cells. Immunity 37, 634–648 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Moro, K. et al. Innate production of TH2 cytokines by adipose tissue-associated c-Kit+Sca-1+ lymphoid cells. Nature 463, 540–544 (2010).

    CAS  PubMed  Google Scholar 

  46. Yokota, Y. et al. Development of peripheral lymphoid organs and natural killer cells depends on the helix-loop-helix inhibitor Id2. Nature 397, 702–706 (1999).

    CAS  PubMed  Google Scholar 

  47. Sambandam, A. et al. Notch signaling controls the generation and differentiation of early T lineage progenitors. Nat. Immunol. 6, 663–670 (2005).

    CAS  PubMed  Google Scholar 

  48. Yamamoto, N. et al. Role of Deltex-1 as a transcriptional regulator downstream of the Notch receptor. J. Biol. Chem. 276, 45031–45040 (2001).

    CAS  PubMed  Google Scholar 

  49. Rothenberg, E.V. Transcriptional drivers of the T-cell lineage program. Curr. Opin. Immunol. 24, 132–138 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Hobeika, E. et al. Testing gene function early in the B cell lineage in mb1-cre mice. Proc. Natl. Acad. Sci. USA 103, 13789–13794 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank J.C. Zuniga-Pfucker (University of Toronto) for OP9 and OP9-DL1 cells; J. Kisielow (Eidgenossische Technische Hochschule) for the Beko pre-T cell line; M. Busslinger (Institute of Molecular Pathology, Vienna) for Pax5−/− mice; H. Singh (Genentech) for discussions and advice about the culture of Ebf1−/− pre-pro-B cells; I. Falk, S. Fietze and U. Stauffer for help with flow cytometry, genotyping and intravenous injection of mice; A. Rolink, J. Kirberg and F. Savarese and members of the Grosschedl laboratory for discussions; D. van Essen for critical comments on the manuscript; and M. Rott for help in preparing the figures and manuscript. Supported by the Max Planck Society (R.G.) and the German Research Foundation (R.G. and A.D.).

Author information

Authors and Affiliations

  1. Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany

    Robert Nechanitzky, Duygu Akbas, Stefanie Scherer, Ildiko Györy, Senthilkumar Ramamoorthy & Rudolf Grosschedl

  2. Institute of Medical Microbiology and Hygiene, University of Freiburg, Freiburg, Germany

    Thomas Hoyler & Andreas Diefenbach

Authors
  1. Robert Nechanitzky
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Duygu Akbas
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Stefanie Scherer
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ildiko Györy
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Thomas Hoyler
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Senthilkumar Ramamoorthy
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Andreas Diefenbach
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Rudolf Grosschedl
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

R.N. designed and did experiments, analyzed data and wrote the manuscript; D.A., S.S. and T.H. did experiments and analyzed data; S.R. did bioinformatic analysis; I.G. provided Ebf1fl mice; A.D. supervised research; and R.G. designed and supervised research and wrote the manuscript.

Corresponding author

Correspondence to Rudolf Grosschedl.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Figures and Tables

Supplementary Figures 1–6 and Supplementary Tables 1 and 2 (PDF 1120 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Nechanitzky, R., Akbas, D., Scherer, S. et al. Transcription factor EBF1 is essential for the maintenance of B cell identity and prevention of alternative fates in committed cells. Nat Immunol 14, 867–875 (2013). https://doi.org/10.1038/ni.2641

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ni.2641

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing