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Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

Nature Genetics volume 44, pages 148–156 (2012)Cite this article

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Abstract

Chromatin modifications are associated with many aspects of gene expression, yet their role in cellular transitions during development remains elusive. Here, we use a new approach to obtain cell type–specific information on chromatin state and RNA polymerase II (Pol II) occupancy within the multicellular Drosophila melanogaster embryo. We directly assessed the relationship between chromatin modifications and the spatio-temporal activity of enhancers. Rather than having a unique chromatin state, active developmental enhancers show heterogeneous histone modifications and Pol II occupancy. Despite this complexity, combined chromatin signatures and Pol II presence are sufficient to predict enhancer activity de novo. Pol II recruitment is highly predictive of the timing of enhancer activity and seems dependent on the timing and location of transcription factor binding. Chromatin modifications typically demarcate large regulatory regions encompassing multiple enhancers, whereas local changes in nucleosome positioning and Pol II occupancy delineate single active enhancers. This cell type–specific view identifies dynamic enhancer usage, an essential step in deciphering developmental networks.

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Figure 1: BiTS-ChIP facilitates cell type–specific ChIP in a multicellular context.
Figure 2: BiTS-ChIP has high tissue specificity and sensitivity.
Figure 3: Chromatin marks and Pol II presence are highly correlated with enhancer activity.
Figure 4: Pol II occupancy and local nucleosome positioning identify temporal enhancer activity.
Figure 5: Modeling chromatin state on enhancers to predict enhancer activity.
Figure 6: Predicted active regulatory regions function as enhancers in vivo.

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Acknowledgements

This work was technically supported by the EMBL Genomics Core facility for Solexa sequencing and by the IT service unit. We thank S. Müller for performing Drosophila injections and all members of the Furlong laboratory for discussions and comments on the manuscript. We thank J. Lis (Cornell University) for the Rpb3 (Pol II) antibody. This work was supported by grants to E.E.M.F. from ERASysBio (Mod Heart) and the Human Frontiers Science Program Organization and by a long-term fellowship to R.P.Z. from the International Human Frontiers Science Program Organization. S.B. was funded by the EMBL Interdisciplinary Postdoc (EIPOD) programme.

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  1. Stefan Bonn, Robert P Zinzen and Charles Girardot: These authors contributed equally to this work.

Authors and Affiliations

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

    Stefan Bonn, Robert P Zinzen, Charles Girardot, E Hilary Gustafson, Alexis Perez-Gonzalez, Nicolas Delhomme, Yad Ghavi-Helm, Bartek Wilczyński, Andrew Riddell & Eileen E M Furlong

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Contributions

S.B., R.P.Z. and E.E.M.F. designed the study. S.B., R.P.Z., E.H.G., Y.G.-H., A.P.-G. and A.R. conducted experiments. S.B., R.P.Z., A.P.-G. and A.R. performed FACS sorting. S.B. and R.P.Z. performed the BiTS-ChIP-Seq. C.G., S.B. and N.D. performed computational analyses. B.W. helped with the Bayesian modeling. S.B., C.G., R.P.Z. and E.E.M.F. wrote the manuscript.

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Correspondence to Eileen E M Furlong.

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Supplementary information

Supplementary Text and Figures

Supplementary Note, Supplementary Tables 3, 5, 6 and 8 and Supplementary Figures 1–13. (PDF 6437 kb)

Supplementary Table 1

CAD2 entries in tabular format (XLS 251 kb)

Supplementary Table 2

CAD2 entry list filtered for genes and potential unannotated TSSs (XLS 103 kb)

Supplementary Table 4

112 BNfinder predictions (XLS 67 kb)

Supplementary Table 7

Genes grouped by spatio-temporal activity (XLS 487 kb)

Supplementary Table 9

Histone modification and PolII intensities on CAD2 enhancers (XLS 52 kb)

Supplementary Table 10

BNfinder input file (XLSX 57 kb)

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Bonn, S., Zinzen, R., Girardot, C. et al. Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nat Genet 44, 148–156 (2012). https://doi.org/10.1038/ng.1064

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