Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development
Stefan Bonn, Robert P Zinzen, Charles Girardot, E Hilary Gustafson, Alexis Perez-Gonzalez, Nicolas Delhomme, Yad Ghavi-Helm, Bartek Wilczynski, Andrew Riddell, Eileen EM Furlong
NATURE GENETICS | NATURE PUBLISHING GROUP | Published : 2012
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 enhan..View full abstract
This work was technically supported by the EMBL Genomics Core facility for Solexa sequencing and by the IT service unit. We thank S. Muller 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.