Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

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Abstract

The functional importance of gene enhancers in regulated gene expression is well established1,2,3. In addition to widespread transcription of long non-coding RNAs (lncRNAs) in mammalian cells4,5,6, bidirectional ncRNAs are transcribed on enhancers, and are thus referred to as enhancer RNAs (eRNAs)7,8,9. However, it has remained unclear whether these eRNAs are functional or merely a reflection of enhancer activation. Here we report that in human breast cancer cells 17β-oestradiol (E2)-bound oestrogen receptor α (ER-α) causes a global increase in eRNA transcription on enhancers adjacent to E2-upregulated coding genes. These induced eRNAs, as functional transcripts, seem to exert important roles for the observed ligand-dependent induction of target coding genes, increasing the strength of specific enhancer–promoter looping initiated by ER-α binding. Cohesin, present on many ER-α-regulated enhancers even before ligand treatment, apparently contributes to E2-dependent gene activation, at least in part by stabilizing E2/ER-α/eRNA-induced enhancer–promoter looping. Our data indicate that eRNAs are likely to have important functions in many regulated programs of gene transcription.

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Figure 1: E2 induction of eRNA in MCF-7 breast cancer cells.
Figure 2: Importance of eRNA for target gene activation.
Figure 3: Ligand-induced eRNA is functionally important.
Figure 4: Role of eRNA in cohesin-dependent gene activation.

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Accessions

Gene Expression Omnibus

Data deposits

The sequencing data sets are deposited in the Gene Expression Omnibus database under accession GSE45822.

Change history

  • 04 June 2013

    The PDF was corrected to remove two duplicated references from the Methods reference list.

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Acknowledgements

We thank K. Hutt for help with statistical analyses; M. Ghassemian from the University of California, San Diego (UCSD) Biomolecular/Proteomics Mass Spectrometry Facility for assistance with mass spectrometry; C. Nelson for cell culture assistance; J. Hightower for assistance with figure and manuscript preparation. We thank H. Chang for providing the BoxB, λN–GAL4 constructs. We acknowledge the UCSD Cancer Center Specialized Support Grant P30 CA23100 for confocal microscopy. W.L. and D.N. are supported by Department of Defense (DoD) postdoctoral fellowships, BC110381 and BC103858, respectively. M.G.R. is an investigator with the Howard Hughes Medical Institute. This work was supported by grants DK 039949, DK018477, NS034934, HL065445, CA173903 to C.K.G., and from the DoD.

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M.G.R., W.L., D.N., E.N. and C.K.G. conceived the project. W.L. and D.N. performed most of the experiments reported, with contributions from E.N. and A.Y.C. (FISH). Q.M., B.T. and D.M. performed bioinformatic analyses. Q.M., E.N. and B.T. made equivalent contributions to this study. Additional experiments/methods were contributed by X.S., S.O. and H.-S.K. J.Z. and K.O. assisted in deep-sequencing library preparations and sequencing. W.L., D.N. and M.G.R. wrote the final paper with input from C.K.G.

Corresponding author

Correspondence to Michael G. Rosenfeld.

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The authors declare no competing financial interests.

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Li, W., Notani, D., Ma, Q. et al. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 498, 516–520 (2013). https://doi.org/10.1038/nature12210

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