Letter | Published:

Genetic variants regulating expression levels and isoform diversity during embryogenesis

Nature volume 541, pages 402406 (19 January 2017) | Download Citation


Embryonic development is driven by tightly regulated patterns of gene expression, despite extensive genetic variation among individuals. Studies of expression quantitative trait loci1,2,3,4 (eQTL) indicate that genetic variation frequently alters gene expression in cell-culture models and differentiated tissues5,6. However, the extent and types of genetic variation impacting embryonic gene expression, and their interactions with developmental programs, remain largely unknown. Here we assessed the effect of genetic variation on transcriptional (expression levels) and post-transcriptional (3′ RNA processing) regulation across multiple stages of metazoan development, using 80 inbred Drosophila wild isolates7, identifying thousands of developmental-stage-specific and shared QTL. Given the small blocks of linkage disequilibrium in Drosophila7,8,9, we obtain near base-pair resolution, resolving causal mutations in developmental enhancers, validated transcription-factor-binding sites and RNA motifs. This fine-grain mapping uncovered extensive allelic interactions within enhancers that have opposite effects, thereby buffering their impact on enhancer activity. QTL affecting 3′ RNA processing identify new functional motifs leading to transcript isoform diversity and changes in the lengths of 3′ untranslated regions. These results highlight how developmental stage influences the effects of genetic variation and uncover multiple mechanisms that regulate and buffer expression variation during embryogenesis.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


Primary accessions


  1. 1.

    et al. The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nature Genet. 29, 389–395 (2001)

  2. 2.

    et al. Genetics of gene expression surveyed in maize, mouse and man. Nature 422, 297–302 (2003)

  3. 3.

    et al. Mapping determinants of human gene expression by regional and genome-wide association. Nature 437, 1365–1369 (2005)

  4. 4.

    et al. Population genomics of human gene expression. Nature Genet. 39, 1217–1224 (2007)

  5. 5.

    et al. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464, 768–772 (2010)

  6. 6.

    et al. Patterns of cis regulatory variation in diverse human populations. PLoS Genet. 8, e1002639 (2012)

  7. 7.

    et al. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines. Genome Res. 24, 1193–1208 (2014)

  8. 8.

    et al. Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing. Genome Res. 23, 568–579 (2013)

  9. 9.

    et al. Genomic variation and its impact on gene expression in Drosophila melanogaster. PLoS Genet. 8, e1003055 (2012)

  10. 10.

    et al. The developmental transcriptome of Drosophila melanogaster. Nature 471, 473–479 (2011)

  11. 11.

    et al. Extensive alternative polyadenylation during zebrafish development. Genome Res. 22, 2054–2066 (2012)

  12. 12.

    et al. A quantitative atlas of polyadenylation in five mammals. Genome Res. 22, 1173–1183 (2012)

  13. 13.

    et al. Global patterns of tissue-specific alternative polyadenylation in Drosophila. Cell Reports 1, 277–289 (2012)

  14. 14.

    et al. Diversity and dynamics of the Drosophila transcriptome. Nature 512, 393–399 (2014)

  15. 15.

    et al. A mixed-model approach for genome-wide association studies of correlated traits in structured populations. Nature Genet. 44, 1066–1071 (2012)

  16. 16.

    , , & Efficient set tests for the genetic analysis of correlated traits. Nature Methods 12, 755–758 (2015)

  17. 17.

    , , & Genetic dissection of transcriptional regulation in budding yeast. Science 296, 752–755 (2002)

  18. 18.

    & The maternal-to-zygotic transition: a play in two acts. Development 136, 3033–3042 (2009)

  19. 19.

    , , & LIMIX: genetic analysis of multiple traits. Preprint at (2015)

  20. 20.

    , & Spatial expression of Drosophila Glutathione S-transferase-D1 in the alimentary canal is regulated by the overlying visceral mesoderm. Dev. Growth Differ. 41, 699–702 (1999)

  21. 21.

    et al. Enhancer loops appear stable during development and are associated with paused polymerase. Nature 512, 96–100 (2014)

  22. 22.

    et al. Genome-scale functional characterization of Drosophila developmental enhancers in vivo. Nature 512, 91–95 (2014)

  23. 23.

    , , & Genetics and regulatory impact of alternative polyadenylation in human B-lymphoblastoid cells. PLoS Genet. 8, e1002882 (2012)

  24. 24.

    et al. Tra2 protein biology and mechanisms of splicing control. Biochem. Soc. Trans. 42, 1152–1158 (2014)

  25. 25.

    , , , & Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites. Science 320, 1643–1647 (2008)

  26. 26.

    et al. Neural-specific elongation of 3′ UTRs during Drosophila development. Proc. Natl Acad. Sci. USA 108, 15864–15869 (2011)

  27. 27.

    , , , & Progressive lengthening of 3′untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc. Natl Acad. Sci. USA 106, 7028–7033 (2009)

  28. 28.

    , & ELAV mediates 3′ UTR extension in the Drosophila nervous system. Genes Dev. 26, 2259–2264 (2012)

  29. 29.

    et al. Natural variation in gene expression modulates the severity of mutant phenotypes. Cell 162, 391–402 (2015)

  30. 30.

    , , & Rare and common regulatory variation in population-scale sequenced human genomes. PLoS Genet. 7, e1002144 (2011)

  31. 31.

    , , , & Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nature Protocols 7, 500–507 (2012)

  32. 32.

    et al. Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq. PLoS Biol. 9, e1000590 (2011)

Download references


This work was supported technically by the European Molecular Biology Laboratory (EMBL) Genomics Core facility, and financially by the European Research Council (ERC; FP/2007-2013), ERC advanced grant CisRegVar to E.E.M.F., EMBL predoctoral funds to E.E.M.F. and E.B.

Author information

Author notes

    • Enrico Cannavò
    •  & Nils Koelling

    These authors contributed equally to this work.


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

    • Enrico Cannavò
    • , Dermot Harnett
    • , David Garfield
    • , Lucia Ciglar
    • , Hilary E. Gustafson
    • , Rebecca R. Viales
    • , Raquel Marco-Ferreres
    • , Jacob F. Degner
    • , Bingqing Zhao
    •  & Eileen E. M. Furlong
  2. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK

    • Nils Koelling
    • , Francesco P. Casale
    • , Oliver Stegle
    •  & Ewan Birney


  1. Search for Enrico Cannavò in:

  2. Search for Nils Koelling in:

  3. Search for Dermot Harnett in:

  4. Search for David Garfield in:

  5. Search for Francesco P. Casale in:

  6. Search for Lucia Ciglar in:

  7. Search for Hilary E. Gustafson in:

  8. Search for Rebecca R. Viales in:

  9. Search for Raquel Marco-Ferreres in:

  10. Search for Jacob F. Degner in:

  11. Search for Bingqing Zhao in:

  12. Search for Oliver Stegle in:

  13. Search for Ewan Birney in:

  14. Search for Eileen E. M. Furlong in:


E.E.M.F., E.B., E.C. and N.K. designed the study, explored results and prepared the manuscript, with contributions from all authors. E.C. led the experiments with help from L.C., H.E.G., R.R.V., R.M.-F. and B.Z. N.K. led the data processing and QTL calling, with help from F.P.C., J.F.D. and O.S. D.H. led the biological analysis, with input from D.G and N.K.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Ewan Birney or Eileen E. M. Furlong.

Reviewer Information Nature thanks S. Celniker and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains a detailed description of the experimental and computational methods.

Zip files

  1. 1.

    Supplementary Data

    This file contains Supplementary Tables 1-14.

About this article

Publication history






Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.