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Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation


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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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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.


  1. Newman, J. J. & Young, R. A. Connecting transcriptional control to chromosome structure and human disease. Cold Spring Harb. Symp. Quant. Biol. 75, 227–235 (2010)

    Article  CAS  Google Scholar 

  2. Bulger, M. & Groudine, M. Functional and mechanistic diversity of distal transcription enhancers. Cell 144, 327–339 (2011)

    Article  CAS  Google Scholar 

  3. Ong, C. T. & Corces, V. G. Enhancer function: new insights into the regulation of tissue-specific gene expression. Nature Rev. Genet. 12, 283–293 (2011)

    Article  CAS  Google Scholar 

  4. Guttman, M. & Rinn, J. L. Modular regulatory principles of large non-coding RNAs. Nature 482, 339–346 (2012)

    Article  ADS  CAS  Google Scholar 

  5. Wang, K. C. & Chang, H. Y. Molecular mechanisms of long noncoding RNAs. Mol. Cell 43, 904–914 (2011)

    Article  CAS  Google Scholar 

  6. Mercer, T. R., Dinger, M. E. & Mattick, J. S. Long non-coding RNAs: insights into functions. Nature Rev. Genet. 10, 155–159 (2009)

    Article  CAS  Google Scholar 

  7. Kim, T.-K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182–187 (2010)

    Article  ADS  CAS  Google Scholar 

  8. Hah, N. et al. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell 145, 622–634 (2011)

    Article  CAS  Google Scholar 

  9. Wang, D. et al. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474, 390–394 (2011)

    Article  CAS  Google Scholar 

  10. Welboren, W. J. et al. ChIP-Seq of ERα and RNA polymerase II defines genes differentially responding to ligands. EMBO J. 28, 1418–1428 (2009)

    Article  CAS  Google Scholar 

  11. Carroll, J. S. et al. Genome-wide analysis of estrogen receptor binding sites. Nature Genet. 38, 1289–1297 (2006)

    Article  CAS  Google Scholar 

  12. Kwon, Y. S. et al. Sensitive ChIP-DSL technology reveals an extensive estrogen receptor α-binding program on human gene promoters. Proc. Natl Acad. Sci. USA 104, 4852–4857 (2007)

    Article  ADS  CAS  Google Scholar 

  13. Heintzman, N. D. & Ren, B. Finding distal regulatory elements in the human genome. Curr. Opin. Genet. Dev. 19, 541–549 (2009)

    Article  CAS  Google Scholar 

  14. Heintzman, N. D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108–112 (2009)

    Article  ADS  CAS  Google Scholar 

  15. Creyghton, M. P. et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl Acad. Sci. USA 107, 21931–21936 (2010)

    Article  ADS  CAS  Google Scholar 

  16. Ahlenstiel, C. L. et al. Direct evidence of nuclear Argonaute distribution during transcriptional silencing links the actin cytoskeleton to nuclear RNAi machinery in human cells. Nucleic Acids Res. 40, 1579–1595 (2012)

    Article  CAS  Google Scholar 

  17. Mayer, C., Schmitz, K. M., Li, J., Grummt, I. & Santoro, R. Intergenic transcripts regulate the epigenetic state of rRNA genes. Mol. Cell 5, 351–361 (2006)

    Article  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  19. Melo, C. A. et al. eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol. Cell 49, 524–535 (2013)

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  21. Fullwood, M. J. et al. An oestrogen-receptor-α-bound human chromatin interactome. Nature 462, 58–64 (2009)

    Article  ADS  CAS  Google Scholar 

  22. Harismendy, O. et al. 9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. Nature 470, 264–268 (2011)

    Article  ADS  CAS  Google Scholar 

  23. Sanyal, A., Lajoie, B. R., Jain, G. & Dekker, J. The long-range interaction landscape of gene promoters. Nature 489, 109–113 (2012)

    Article  ADS  CAS  Google Scholar 

  24. Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009)

    Article  ADS  CAS  Google Scholar 

  25. Chu, C., Qu, K., Zhong, F. L., Artandi, S. E. & Chang, H. Y. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol. Cell 44, 667–678 (2011)

    Article  CAS  Google Scholar 

  26. Hadjur, S. et al. Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus. Nature 460, 410–413 (2009)

    Article  ADS  CAS  Google Scholar 

  27. Kagey, M. H. et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 467, 430–435 (2010)

    Article  ADS  CAS  Google Scholar 

  28. Schmidt, D. et al. A CTCF-independent role for cohesin in tissue-specific transcription. Genome Res. 20, 578–588 (2010)

    Article  CAS  Google Scholar 

  29. Cai, S. & Kohwi-Shigematsu, T. Intranuclear relocalization of matrix binding sites during T cell activation detected by amplified fluorescence in situ hybridization. Methods 19, 394–402 (1999)

    Article  CAS  Google Scholar 

  30. Core, L. J., Waterfall, J. J. & Lis, J. T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845–1848 (2008)

    Article  ADS  CAS  Google Scholar 

  31. Abukhdeir, A. M. et al. Physiologic estrogen receptor α signaling in non-tumorigenic human mammary epithelial cells. Breast Cancer Res. Treat. 99, 23–33 (2006)

    Article  CAS  Google Scholar 

  32. Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010)

    Article  CAS  Google Scholar 

  33. Ingolia, N. T. et al. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218–223 (2009)

    Article  ADS  CAS  Google Scholar 

  34. White, A. K. et al. High-throughput microfluidic single-cell RT-qPCR. Proc. Natl Acad. Sci. USA 108, 13999–14004 (2011)

    Article  ADS  CAS  Google Scholar 

  35. Zhong, J. F. et al. A microfluidic processor for gene expression profiling of single human embryonic stem cells. Lab Chip 8, 68–74 (2008)

    Article  CAS  Google Scholar 

  36. Tsai, M. C. et al. Long non-coding RNA as modular scaffold of histone modification complexes. Science 329, 689–693 (2010)

    Article  ADS  CAS  Google Scholar 

  37. Rueden, C. T. et al. Visualization approaches for multidimensional biological image data. Biotechniques 43, 31–36 (2007)

    Article  Google Scholar 

  38. Lajoie, B. R. et al. My5C: web tools for chromosome conformation capture studies. Nature Methods 6, 690–691 (2009)

    Article  CAS  Google Scholar 

  39. Servant, N. et al. HiTC: exploration of high-throughput ‘C’ experiments. Bioinformatics 28, 2843–2844 (2012)

    Article  CAS  Google Scholar 

  40. Stadhouders, R. et al. Dynamic long-range chromatin interactions control Myb proto-oncogene transcription during erythroid development. EMBO J. 31, 986–999 (2011)

    Article  Google Scholar 

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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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Authors and Affiliations



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.

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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).

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