Article | Published:

Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution

Nature Genetics volume 46, pages 685692 (2014) | Download Citation

Abstract

Phenotypic differences between closely related species are thought to arise primarily from changes in gene expression due to mutations in cis-regulatory sequences (enhancers). However, it has remained unclear how frequently mutations alter enhancer activity or create functional enhancers de novo. Here we use STARR-seq, a recently developed quantitative enhancer assay, to determine genome-wide enhancer activity profiles for five Drosophila species in the constant trans-regulatory environment of Drosophila melanogaster S2 cells. We find that the functions of a large fraction of D. melanogaster enhancers are conserved for their orthologous sequences owing to selection and stabilizing turnover of transcription factor motifs. Moreover, hundreds of enhancers have been gained since the D. melanogasterDrosophila yakuba split about 11 million years ago without apparent adaptive selection and can contribute to changes in gene expression in vivo. Our finding that enhancer activity is often deeply conserved and frequently gained provides functional insights into regulatory evolution.

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Acknowledgements

We thank the Drosophila Species Stock Center (DSSC) at the University of California, San Diego for genomic DNA, I. Sinitsyn and Ł.M. Boryń for help with library cloning, M. Rath, K. Schernhuber and O. Frank for help with experiments, J.O. Yáñez-Cuna and M.A. Zabidi for help with data analysis, and S. Westermann, L. Cochella, I. Crisostomo, J. Brennecke, J. Knoblich, U. Technau, K. Tessmar-Raible and F. Raible for comments on the manuscript. Deep sequencing was performed at the CSF (Campus Science Support Facilities) Next-Generation Sequencing Unit and the Brandeis Genomics Core Facility (laboratory of M. Rosbash). C.D.A. is supported by a European Research Council (ERC) Starting Grant (242922) awarded to A.S. This work was partly supported by the Austrian Science Fund (FWF), F4303-B09. The work of N.C.L. was supported by the Searle Scholars foundation and the US National Institutes of Health (HD057298). Basic research at IMP is supported by Boehringer Ingelheim.

Author information

Author notes

    • Daniel Gerlach
    •  & Jessica A Matts

    Present addresses: Boehringer Ingelheim, Vienna, Austria (D.G.) and Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, USA (J.A.M.).

    • Cosmas D Arnold
    •  & Daniel Gerlach

    These authors contributed equally to this work.

Affiliations

  1. Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.

    • Cosmas D Arnold
    • , Daniel Gerlach
    • , Daniel Spies
    • , Michaela Pagani
    •  & Alexander Stark
  2. Department of Biology, Brandeis University, Waltham, Massachusetts, USA.

    • Jessica A Matts
    • , Yuliya A Sytnikova
    •  & Nelson C Lau
  3. Rosenstiel Basic Medical Science Research Center at Brandeis University, Waltham, Massachusetts, USA.

    • Jessica A Matts
    • , Yuliya A Sytnikova
    •  & Nelson C Lau

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Contributions

C.D.A. and A.S. conceived the project. C.D.A., D.S. and M.P. performed the experiments. J.A.M., Y.A.S. and N.C.L. generated the follicle cell RNA-seq data. D.G. and A.S. conducted all computational experiments and bioinformatics analyses. C.D.A., D.G. and A.S. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Alexander Stark.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Tables 1, 3 and 5, and Supplementary Figures 1–15

Excel files

  1. 1.

    Supplementary Table 2

    TF motif conservation in functionally conserved and D. melanogaster–specific S2 cell enhancers.

  2. 2.

    Supplementary Table 4

    RNA-seq in follicle cells—gene expression (RPKM) values.

Zip files

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    Supplementary Data Set 1

    STARR-seq peak calls

About this article

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DOI

https://doi.org/10.1038/ng.3009

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