Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments

Abstract

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.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: Chromatin 3D structure brings H3K4me3-primed TNF-responsive genes proximal to IPLs.
Fig. 2: UMLILO is a new super-enhancer-resident lncRNA that is transcribed within the ELR + CXC chemokine TAD.
Fig. 3: The UMLILO lncRNA regulates H3K4me3 across the CXCL chemokine promoters.
Fig. 4: UMLILO interacts with WDR5.
Fig. 5: UMLILO acts in cis to regulate chemokine transcription.
Fig. 6: WDR5–lncRNA regulation is a general mechanism of H3K4me3-primed TNF-responsive genes.
Fig. 7: β-Glucan epigenetically reprograms immune genes by upregulating IPLs in a NFAT-dependent manner.
Fig. 8: Inserting UMLILO within the mouse chemokine TAD restored training of the Cxcl chemokines.

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.

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.

References

  1. 1.

    Rogatsky, I. & Adelman, K. Preparing the first responders: building the inflammatory transcriptome from the ground up. Mol. Cell 54, 245–254 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. 2.

    Bhatt, D. M. et al. Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell 150, 279–290 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. 3.

    Lauberth, S. M. et al. H3K4me3 interactions with TAF3 regulate preinitiation complex assembly and selective gene activation. Cell 152, 1021–1036 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. 4.

    Quintin, J. et al. Candida albicans infection affords protection against reinfection via functional reprogramming of monocytes. Cell Host Microbe 12, 223–232 (2012).

    CAS  PubMed  Google Scholar 

  5. 5.

    Saeed, S. et al. Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity. Science 345, 1251086 (2014).

    PubMed  PubMed Central  Google Scholar 

  6. 6.

    Netea, M. G. et al. Trained immunity: a program of innate immune memory in health and disease. Science 352, 6284 (2016).

    Google Scholar 

  7. 7.

    Arts, R. J. et al. Glutaminolysis and fumarate accumulation integrate immunometabolic and epigenetic programs in trained immunity. Cell Metab. 24, 807–819 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Novakovic, B. et al. β-Glucan reverses the epigenetic state of LPS-induced immunological tolerance. Cell 167, 1354–1368 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. 9.

    Li, G. et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148, 84–98 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. 10.

    Fanucchi, S. et al. Chromosomal contact permits transcription between coregulated genes. Cell 155, 606–620 (2013).

    CAS  PubMed  Google Scholar 

  11. 11.

    Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. 12.

    Jin, F. et al. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 503, 290–294 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. 13.

    Nora, E. P. et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485, 381–385 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. 14.

    Dixon, J. R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. 15.

    Dekker, J. & Mirny, L. The 3D genome as moderator of chromosomal communication. Cell 164, 1110–1121 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. 16.

    Guttman, M. et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477, 295–300 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17.

    Gomez, J. A. et al. The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-γ locus. Cell 152, 743–754 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. 18.

    Quinodoz, S. & Guttman, M. Long noncoding RNAs: an emerging link between gene regulation and nuclear organization. Trends Cell Biol. 24, 651–663 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. 19.

    Andersson, R. et al. An atlas of active enhancers across human cell types and tissues. Nature 507, 455–461 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. 20.

    Lai, F. et al. Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 494, 497–501 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. 21.

    Wang, K. C. et al. A long non-coding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472, 120–124 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. 22.

    Yang, Y. W. et al. Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency. eLife 3, e02046 (2014).

    PubMed  PubMed Central  Google Scholar 

  23. 23.

    Paulsen, M. T. et al. Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response. Proc. Natl Acad. Sci. USA 110, 2240–2245 (2013).

    CAS  PubMed  Google Scholar 

  24. 24.

    Brown, J. D. et al. NF-κB directs dynamic super enhancer formation in inflammation and atherogenesis. Mol. Cell 56, 219–231 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. 25.

    Papantonis, A. et al. TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed. EMBO J. 31, 4404–4414 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. 26.

    Matsushima, K. & Morishita, K. Molecular cloning of a human monocyte-derived neutrophil chemotactic factor (MDNCF) and the induction of MDNCF mRNA by interleukin 1 and tumor necrosis factor. J. Exp. Med. 167, 1883–1893 (1988).

    CAS  PubMed  Google Scholar 

  27. 27.

    Whyte, W. A. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307–319 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. 28.

    Wang, X. et al. MLL1, a H3K4 methyltransferase, regulates the TNFα-stimulated activation of genes downstream of NF-κB. J. Cell Sci. 125, 4058–4066 (2012).

    CAS  PubMed  Google Scholar 

  29. 29.

    Cao, F. et al. Targeting MLL1 H3K4 methyltransferase activity in mixed-lineage leukemia. Mol. Cell 53, 247–261 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. 30.

    Raj, A. et al. Imaging individual mRNA molecules using multiple singly labeled probes. Nat. Methods 5, 877–879 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Shibayama, Y., Fanucchi, S. & Mhlanga, M. M. Visualization of enhancer-derived noncoding RNA. Methods Mol. Biol. 1468, 19–32 (2017).

    CAS  PubMed  Google Scholar 

  32. 32.

    Engreitz, J. M. et al. Local regulation of gene expression by lncRNA promoters, transcription and splicing. Nature 539, 452–455 (2017).

    Google Scholar 

  33. 33.

    Goodridge, H. S. et al. Dectin-1 stimulation by Candida albicans yeast or zymosan triggers NFAT activation in macrophages and dendritic cells. J. Immunol. 178, 3107–3115 (2007).

    CAS  PubMed  Google Scholar 

  34. 34.

    Asfaha, S. et al. Mice that express human interleukin-8 have increased mobilization of immature myeloid cells, which exacerbates inflammation and accelerates colon carcinogenesis. Gastroenterology 144, 155–166 (2013).

    CAS  PubMed  Google Scholar 

  35. 35.

    Sauter, C. & Wolfensberger, C. Interferon in human serum after injection of endotoxin. Lancet 2, 852–853 (1980).

    CAS  PubMed  Google Scholar 

  36. 36.

    Thin, L. W. et al. Oral tacrolimus for the treatment of refractory inflammatory bowel disease in the biologic era. Inflamm. Bowel Dis. 19, 1490–1498 (2013).

    PubMed  Google Scholar 

  37. 37.

    Zemach, A., McDaniel, I. E., Silva, P. & Zilberman, D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328, 916–919 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. 38.

    Kærn, M. et al. Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet. 6, 451–464 (2005).

    PubMed  Google Scholar 

  39. 39.

    Mills, E. L. et al. Succinate dehydrogenase supports metabolic repurposing of mitochondria to drive inflammatory macrophages. Cell 167, 457–470 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. 40.

    Arts, R. J. W. et al. BCG vaccination protects against experimental viral infection in humans through the induction of cytokines associated with trained immunity. Cell Host Microbe 10, 89–100 (2018).

    Google Scholar 

  41. 41.

    Campbell, L. M. et al. Rationale and means to target pro-inflammatory interleukin-8 (CXCL8). Signal. CancerPharmaceut. 6, 929–959 (2013).

    Google Scholar 

  42. 42.

    Repnik, U., Knezevic, M. & Jeras, M. Simple and cost-effective isolation of monocytes from buffy coats. J. Immunol. Methods 278, 283–292 (2003).

    CAS  PubMed  Google Scholar 

  43. 43.

    Imakaev, M. et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat. Methods 9, 999–1003 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Li, G. et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 11, R22 (2010).

    PubMed  PubMed Central  Google Scholar 

  45. 45.

    Tennakoon, C. et al. BatMis: a fast algorithm for k-mismatch mapping. Bioinformatics 28, 2122–2128 (2012).

    CAS  PubMed  Google Scholar 

  46. 46.

    Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. 47.

    Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. 48.

    Chu, C. & Chang, H. Y. Understanding RNA-chromatin interactions using chromatin isolation by RNA purification (ChIRP). Methods Mol. Biol. 1480, 115–123 (2016).

    CAS  PubMed  Google Scholar 

  49. 49.

    Chen, B. et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155, 1479–1491 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. 50.

    Samulski, R. J. et al. A recombinant plasmid from which an infectious adeno-associated virus genome can be excised in vitro and its use to study viral replication. J. Virol. 61, 3096–3101 (1987).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. 51.

    Grimm, D. Production methods for gene transfer vectors based on adeno-associated virus serotypes. Methods 28, 146–157 (2002).

    CAS  PubMed  Google Scholar 

  52. 52.

    Grimm, D. et al. In vitro and in vivo gene therapy vector evolution via multi species interbreeding and retargeting of adeno-associated viruses. J. Virol. 82, 5887–5911 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. 53.

    Shevchenko, A. et al. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protoc. 1, 2856–2860 (2007).

    Google Scholar 

  54. 54.

    Hagege, H. et al. Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat. Protoc. 2, 1722–1733 (2007).

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

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

Affiliations

Authors

Contributions

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.

Corresponding author

Correspondence to Musa M. Mhlanga.

Ethics declarations

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).

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–18

Reporting Summary

Supplementary Table 1

Coordinates and tissue-specific expression of the IPLs

Supplementary Table 2

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

Supplementary Table 3

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

Supplementary Table 4

List of siRNA, LNA and oligonucleotide sequences

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Fanucchi, S., Fok, E.T., Dalla, E. et al. Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments. Nat Genet 51, 138–150 (2019). https://doi.org/10.1038/s41588-018-0298-2

Download citation

Further reading