Letter | Published:

Integrator mediates the biogenesis of enhancer RNAs

Nature volume 525, pages 399403 (17 September 2015) | Download Citation

Abstract

Integrator is a multi-subunit complex stably associated with the carboxy-terminal domain (CTD) of RNA polymerase II (RNAPII)1. Integrator is endowed with a core catalytic RNA endonuclease activity, which is required for the 3′-end processing of non-polyadenylated, RNAPII-dependent, uridylate-rich, small nuclear RNA genes1. Here we examine the requirement of Integrator in the biogenesis of transcripts derived from distal regulatory elements (enhancers) involved in tissue- and temporal-specific regulation of gene expression in metazoans2,3,4,5. Integrator is recruited to enhancers and super-enhancers in a stimulus-dependent manner. Functional depletion of Integrator subunits diminishes the signal-dependent induction of enhancer RNAs (eRNAs) and abrogates stimulus-induced enhancer–promoter chromatin looping. Global nuclear run-on and RNAPII profiling reveals a role for Integrator in 3′-end cleavage of eRNA primary transcripts leading to transcriptional termination. In the absence of Integrator, eRNAs remain bound to RNAPII and their primary transcripts accumulate. Notably, the induction of eRNAs and gene expression responsiveness requires the catalytic activity of Integrator complex. We propose a role for Integrator in biogenesis of eRNAs and enhancer function in metazoans.

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Accessions

Primary accessions

Gene Expression Omnibus

Data deposits

High-throughput data are deposited at the Gene Expression Omnibus (GEO) under accession number GSE68401.

References

  1. 1.

    et al. Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II. Cell 123, 265–276 (2005)

  2. 2.

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

  3. 3.

    et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 143, 46–58 (2010)

  4. 4.

    et al. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol. 8, e1000384 (2010)

  5. 5.

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

  6. 6.

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

  7. 7.

    et al. Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. Nature 498, 511–515 (2013)

  8. 8.

    et al. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 498, 516–520 (2013)

  9. 9.

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

  10. 10.

    et al. Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc. Natl Acad. Sci. USA 110, 2876–2881 (2013)

  11. 11.

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

  12. 12.

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

  13. 13.

    et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 153, 320–334 (2013)

  14. 14.

    et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934–947 (2013)

  15. 15.

    , , & The long-range interaction landscape of gene promoters. Nature 489, 109–113 (2012)

  16. 16.

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

  17. 17.

    et al. eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. Mol. Cell 51, 606–617 (2013)

  18. 18.

    et al. Integrator regulates transcriptional initiation and pause release following activation. Mol. Cell 56, 128–139 (2014)

  19. 19.

    et al. DSIF and NELF interact with Integrator to specify the correct post-transcriptional fate of snRNA genes. Nat. Commun. 5, 4263 (2014)

  20. 20.

    & snRNA 3′ end formation requires heterodimeric association of integrator subunits. Mol. Cell. Biol. 32, 1112–1123 (2012)

  21. 21.

    et al. Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nature Struct. Mol. Biol. 18, 956–963 (2011)

  22. 22.

    et al. lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs. Nature 500, 598–602 (2013)

  23. 23.

    et al. Integrator complex regulates NELF-mediated RNA polymerase II pause/release and processivity at coding genes. Nat. Commun. 5, 5531 (2014)

  24. 24.

    et al. The Integrator complex controls the termination of transcription at diverse classes of gene targets. Cell Res. 25, 288–305 (2015)

  25. 25.

    et al. Enhancer RNA facilitates NELF release from immediate early genes. Mol. Cell 56, 29–42 (2014)

  26. 26.

    et al. Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91–100 (2012)

  27. 27.

    , , & Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009)

  28. 28.

    , & RSeQC: quality control of RNA-seq experiments. Bioinformatics 28, 2184–2185 (2012)

  29. 29.

    et al. seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res. 39, e35 (2011)

  30. 30.

    , , & ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics 15, 284 (2014)

  31. 31.

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

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Acknowledgements

We would like to thank J. M. Marinis and M. A. Lazar for technical support for GRO-seq experiments. We thank D. Hu in A. Shilatifard’s laboratory for performing the SEC ChIP-seq experiments. We thank the Oncogenomics core facility at Sylvester Comprehensive Cancer Center for performing high-throughput sequencing. We also thank Shiekhattar laboratory members and P.-J. Hamard for support and discussions. This work was supported by funds from University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center and grants R01 GM078455 and R01 GM105754 (R.S.) from the National Institute of Health.

Author information

Author notes

    • Fan Lai
    •  & Alessandro Gardini

    These authors contributed equally to this work.

Affiliations

  1. University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Department of Human Genetics, Biomedical Research Building, Room 719, 1501 NW 10th Avenue, Miami, Florida 33136, USA

    • Fan Lai
    • , Alessandro Gardini
    • , Anda Zhang
    •  & Ramin Shiekhattar

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Contributions

F.L. and A.G. are co-first authors. R.S., F.L. and A.G. conceived and designed the overall project. F.L., A.G. and A.Z. performed the experiments. R.S., F.L. and A.G. analysed the data and wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Ramin Shiekhattar.

Extended data

Supplementary information

Excel files

  1. 1.

    Supplementary Table 1

    This table contains a list of 91 EGF stimulated enhancer RNA loci.

  2. 2.

    Supplementary Table 2

    This table contains all the PCR primer sequences and hairpin sequences.

About this article

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DOI

https://doi.org/10.1038/nature14906

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