Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP
Stefan Bonn, Robert P Zinzen, Alexis Perez-Gonzalez, Andrew Riddell, Anne-Claude Gavin, Eileen EM Furlong
NATURE PROTOCOLS | NATURE PUBLISHING GROUP | Published : 2012
This protocol describes the batch isolation of tissue-specific chromatin for immunoprecipitation (BiTS-ChIP) for analysis of histone modifications, transcription factor binding, or polymerase occupancy within the context of a multicellular organism or tissue. Embryos expressing a cell type-specific nuclear marker are formaldehyde cross-linked and then subjected to dissociation. Fixed nuclei are isolated and sorted using FACS on the basis of the cell type-specific nuclear marker. Tissue-specific chromatin is extracted, sheared by sonication and used for ChIP-seq or other analyses. The key advantages of this method are the covalent cross-linking before embryo dissociation, which preserves the ..View full abstract
We thank E. H. Gustafson for fly work, and J. Erceg for sharing staged, sorted nuclei. We are very grateful to all members of the Furlong Laboratory, J. Mueller, C. Margulies and A. G. Ladurner for helpful discussions. This work was supported by grants to E. E. M. F. from ERASysBio (Mod Heart) and the Human Frontiers Science 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 European Molecular Biology Laboratory Interdisciplinary Postdoctoral Programme.