Letter | Published:

Enhancer loops appear stable during development and are associated with paused polymerase

Nature volume 512, pages 96100 (07 August 2014) | Download Citation

  • A Corrigendum to this article was published on 13 July 2016

Abstract

Developmental enhancers initiate transcription and are fundamental to our understanding of developmental networks, evolution and disease. Despite their importance, the properties governing enhancer–promoter interactions and their dynamics during embryogenesis remain unclear. At the β-globin locus, enhancer–promoter interactions appear dynamic and cell-type specific1,2, whereas at the HoxD locus they are stable and ubiquitous, being present in tissues where the target genes are not expressed3,4. The extent to which preformed enhancer–promoter conformations exist at other, more typical, loci and how transcription is eventually triggered is unclear. Here we generated a high-resolution map of enhancer three-dimensional contacts during Drosophila embryogenesis, covering two developmental stages and tissue contexts, at unprecedented resolution. Although local regulatory interactions are common, long-range interactions are highly prevalent within the compact Drosophila genome. Each enhancer contacts multiple enhancers, and promoters with similar expression, suggesting a role in their co-regulation. Notably, most interactions appear unchanged between tissue context and across development, arising before gene activation, and are frequently associated with paused RNA polymerase. Our results indicate that the general topology governing enhancer contacts is conserved from flies to humans and suggest that transcription initiates from preformed enhancer–promoter loops through release of paused polymerase.

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Accessions

Primary accessions

ArrayExpress

European Nucleotide Archive

Data deposits

All raw data, which consists of 2,587 demultiplexed files, have been submitted to the EBI European Nucleotide Archive and ArrayExpress databases, accession numbers ERP004524 and E-MTAB-2180, respectively. To enable the community to browse through the data, 4C-seq interaction data is available in a customized web browser at http://furlonglab.embl.de/4CBrowser.

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Acknowledgements

This work was technically supported by the EMBL Genomics Core and FACS core facilities. We thank all members of the Furlong laboratory for discussions and comments, in particular D. Garfield, J. Reddington and I. Schor for important suggestions. Embryo images in Fig. 3c were used with permission from Development27 and Nature Publishing Group26 as these fly strains no longer exist. This work was supported by a DFG (FU 750) grant to E.E.M.F., an EMBO post-doctoral fellowship to Y.G.-H., and the EC FP7 project ‘Radiant’ grant to F.A.K. and W.H.

Author information

Author notes

    • Felix A. Klein
    •  & Tibor Pakozdi

    These authors contributed equally to this work.

Affiliations

  1. European Molecular Biology Laboratory, Genome Biology Unit, D-69117 Heidelberg, Germany

    • Yad Ghavi-Helm
    • , Felix A. Klein
    • , Tibor Pakozdi
    • , Lucia Ciglar
    • , Wolfgang Huber
    •  & Eileen E. M. Furlong
  2. Swiss Federal Institute of Technology, School of Life Sciences, CH-1015 Lausanne, Switzerland

    • Daan Noordermeer

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Contributions

Y.G.-H. and E.E.M.F. designed the study, analysed the results and wrote the manuscript. Y.G.-H. performed 4C experiments, DNA in situ hybridization and imaging and performed data analysis. F.A.K., T.P. and W.H. developed and performed 4C-seq bioinformatics analysis. L.C. generated all transgenic strains and performed 4C-PCR reactions, RNA in situ hybridizations and imaging. D.N. was involved in 4C primer design. T.P. and F.A.K. contributed equally to the study. All authors discussed the results and commented on the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Eileen E. M. Furlong.

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https://doi.org/10.1038/nature13417

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