Accumulation of trimethylation of histone H3 at lysine 4 (H3K4me3) on immune-related gene promoters underlies robust transcription during trained immunity. However, the molecular basis for this remains unknown. Here we show three-dimensional chromatin topology enables immune genes to engage in chromosomal contacts with a subset of long noncoding RNAs (lncRNAs) we have defined as immune gene–priming lncRNAs (IPLs). We show that the prototypical IPL, UMLILO, acts in cis to direct the WD repeat-containing protein 5 (WDR5)–mixed lineage leukemia protein 1 (MLL1) complex across the chemokine promoters, facilitating their H3K4me3 epigenetic priming. This mechanism is shared amongst several trained immune genes. Training mediated by β-glucan epigenetically reprograms immune genes by upregulating IPLs in manner dependent on nuclear factor of activated T cells. The murine chemokine topologically associating domain lacks an IPL, and the Cxcl genes are not trained. Strikingly, the insertion of UMLILO into the chemokine topologically associating domain in mouse macrophages resulted in training of Cxcl genes. This provides strong evidence that lncRNA-mediated regulation is central to the establishment of trained immunity.

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Data availability

The data that support the findings of this study are available from the corresponding author upon reasonable request. RNA-seq data are available in the Gene Expression Omnibus under accession number GSE120621.

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Change history

  • 15 January 2019

    In the version of this article initially published, ‘+’ and ‘–’ labels were missing from the graph keys at the bottom of Fig. 8d. The error has been corrected in the HTML and PDF versions of the article.


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We thank all members of the Gene Expression and Biophysics Laboratory (the M.M.M. laboratory). We thank M. Lusic, A Gontijo, F. Brombacher, Y. Negishi, L. Davignon and INTRIM consortium members for comments on the manuscript. The authors also thank S. Consalvi, M. Charpentier, A. Boucharlat and the Chemogenomic and Biological screening core facility at the Institut Pasteur in Paris for support during the course of this work. This research is supported by a Department of Science and Technology Centre of Competence Grant, an SA Medical Research Council SHIP grant, and a CSIR Parliamentary Grant, all to M.M.M., and M.M.M. is a Chan Zuckerberg Investigator of the Chan Zuckerberg Initiative. A full list of the investigators who contributed to the generation of the Blueprint Consortium data used in the ChIP-seq project is available from http://www.blueprint-epigenome.eu. Funding for that project was provided by the European Union’s Seventh Framework Programme (FP7/2007–2013) under grant agreement number 282510–BLUEPRINT.

Author information


  1. Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa

    • Stephanie Fanucchi
    • , Ezio T. Fok
    • , Emiliano Dalla
    • , Youtaro Shibayama
    •  & Musa M. Mhlanga
  2. BTRI, CSIR Biosciences, Pretoria, South Africa

    • Stephanie Fanucchi
    •  & Ezio T. Fok
  3. Department of Medicine, Università degli Studi di Udine, Udine, Italy

    • Emiliano Dalla
  4. RIKEN Center for Integrative Medical Sciences, Yokohama, Japan

    • Youtaro Shibayama
  5. Department of Infectious Diseases/Virology, BioQuant Center, Heidelberg University Hospital, Heidelberg, Germany

    • Kathleen Börner
    •  & Dirk Grimm
  6. Heidelberg Partner Site, German Center for Infection Research (DZIF), Heidelberg, Germany

    • Kathleen Börner
    •  & Dirk Grimm
  7. Department of Dermatology, Stanford University, Stanford, CA, USA

    • Erin Y. Chang
    •  & Kevin C. Wang
  8. Biomedical Technologies Group, CSIR Biosciences, Pretoria, South Africa

    • Stoyan Stoychev
  9. Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Boston, MA, USA

    • Maxim Imakaev
  10. Cluster of Excellence CellNetworks, Heidelberg, Germany

    • Dirk Grimm
  11. College of Informatics, Huazhong Agricultural University, Wuhan, China

    • Guoliang Li
  12. School of Computing, National University of Singapore, Singapore, Singapore

    • Wing-Kin Sung
  13. Genome Institute of Singapore, Singapore, Singapore

    • Wing-Kin Sung
  14. Gene Expression and Biophysics Unit, Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, Lisbon, Portugal

    • Musa M. Mhlanga


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S.F. and M.M.M. designed the study. S.F. performed most experiments and collected and analyzed data. E.T.F. carried out 3C experiments and ChIP and analyzed data. E.D. analyzed CAGE, ChIP and RNA-seq data. Y.S. designed 3C experiments and performed RNA FISH experiments. K.B. and D.G. designed and produced the AAV vectors. E.Y.C. and K.C.W. helped design and perform the UMLILO knock-in experiment. S.S. carried out mass spectrometry experiments and analyzed data. M.I. analyzed Hi-C data. G.L. and W.-K.S. analyzed ChIP and ChIA-PET data. S.F., Y.S., M.I., E.T.F. and M.M.M. discussed and edited the paper. S.F. and M.M.M. co-wrote the paper. M.M.M. designed experiments, analyzed data and supervised the study.

Competing interests

CSIR (Pretoria) has filed a provisional patent application on behalf of S.F., Y.S., E.D. and M.M.M. claiming some of the concepts described in this publication and licensed the patent to Immunolincs Genomics (Seattle, WA).

Corresponding author

Correspondence to Musa M. Mhlanga.

Supplementary information

  1. Supplementary Text and Figures

    Supplementary Figures 1–18

  2. Reporting Summary

  3. Supplementary Table 1

    Coordinates and tissue-specific expression of the IPLs

  4. Supplementary Table 2

    Chromatin interactions between TNF-responsive genes and lncRNAs in unstimulated HUVECs

  5. Supplementary Table 3

    Chromatin interactions between TNF-responsive genes and lncRNAs in HUVECs stimulated with TNF for 30 min

  6. Supplementary Table 4

    List of siRNA, LNA and oligonucleotide sequences

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