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Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

Nature volume 498, pages 511–515 (2013)Cite this article

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Abstract

Rev-Erb-α and Rev-Erb-β are nuclear receptors that regulate the expression of genes involved in the control of circadian rhythm1,2, metabolism3,4 and inflammatory responses5. Rev-Erbs function as transcriptional repressors by recruiting nuclear receptor co-repressor (NCoR)–HDAC3 complexes to Rev-Erb response elements in enhancers and promoters of target genes6,7,8, but the molecular basis for cell-specific programs of repression is not known. Here we present evidence that in mouse macrophages Rev-Erbs regulate target gene expression by inhibiting the functions of distal enhancers that are selected by macrophage-lineage-determining factors, thereby establishing a macrophage-specific program of repression. Remarkably, the repressive functions of Rev-Erbs are associated with their ability to inhibit the transcription of enhancer-derived RNAs (eRNAs). Furthermore, targeted degradation of eRNAs at two enhancers subject to negative regulation by Rev-Erbs resulted in reduced expression of nearby messenger RNAs, suggesting a direct role of these eRNAs in enhancer function. By precisely defining eRNA start sites using a modified form of global run-on sequencing that quantifies nascent 5′ ends, we show that transfer of full enhancer activity to a target promoter requires both the sequences mediating transcription-factor binding and the specific sequences encoding the eRNA transcript. These studies provide evidence for a direct role of eRNAs in contributing to enhancer functions and suggest that Rev-Erbs act to suppress gene expression at a distance by repressing eRNA transcription.

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Figure 1: Rev-Erb binding and function at macrophage-specific enhancers.
Figure 2: Rev-Erb negatively regulates enhancer transcription.
Figure 3: Reduction of eRNA expression results in reduced expression of nearby mRNAs.
Figure 4: eRNA contribution to enhancer activity and consequences of knockdown in vivo.

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Gene Expression Omnibus

Data deposits

Sequencing data have been deposited in the Gene Expression Omnibus under accession GSE45914.

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Acknowledgements

We thank L. Bautista for assistance with figure preparation. These studies were supported by National Institutes of Health grants CA17390, U19DK62434, DK091183, DK063491, CA014195, DK057978, HL088093, HL105278 and CA52599. M.G.R. and R.M.E. are Investigators of the Howard Hughes Medical Institute. M.T.Y.L. is supported by the University of California, San Diego Medical Scientist Training Program T32 GM007198-37, and Genetics Training Program T32 GM008666, National Institute of General Medical Sciences. M.U.K. was supported by a LeDucq Foundation Fellowship. H.P.L. was supported by the Finnish Cultural Foundation, Instumentarium Foundation, The Paulo Foundation, Paavo Nurmi Foundation, Finnish Foundation for Cardiovascular Research, The Maud Kuistila Memorial Foundation and The Fulbright Center. These studies were also supported by grants from the Leona M. and Harry B. Helmsley Charitable Trust, Samuel Waxman Cancer Research Foundation, the Glenn Foundation for Medical Research, the Ellison Medical Foundation and Ipsen/Biomeasure.

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Authors and Affiliations

  1. Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA,

    Michael T. Y. Lam, Hanna P. Lesch, David Gosselin, Sven Heinz, Yumiko Tanaka-Oishi, Christopher Benner, Minna U. Kaikkonen, Mika Kosaka, Cindy Y. Lee & Christopher K. Glass

  2. Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, 92037, California, USA

    Han Cho & Ronald M. Evans

  3. Isis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, USA,

    Aneeza S. Kim, Andy Watt & Tamar R. Grossman

  4. Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA,

    Michael G. Rosenfeld & Christopher K. Glass

  5. Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, 20815-6789, Maryland, USA

    Michael G. Rosenfeld & Ronald M. Evans

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Contributions

M.T.Y.L., S.H., C.B., A.W., T.R.G., M.G.R., R.M.E. and C.K.G. conceived the project and planned experiments, which were performed by M.T.Y.L., H.C., H.P.L., D.G., S.H., Y.T.-O., M.U.K., A.S.K., M.K. and C.Y.L., and analysed by M.T.Y.L., H.P.L., D.G., C.B. and C.K.G. The project was supervised by C.K.G., who wrote the manuscript with M.T.Y.L.

Corresponding author

Correspondence to Christopher K. Glass.

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Competing interests

A.S.K., A.W. and T.R.G. are employees of Isis Pharmaceuticals.

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This file contains Supplementary Figures 1-16 and additional references. (PDF 12417 kb)

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Lam, M., Cho, H., Lesch, H. et al. Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. Nature 498, 511–515 (2013). https://doi.org/10.1038/nature12209

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