Genome-Wide Cell Type-Specific Mapping of In Vivo Chromatin Protein Binding Using an FLP-Inducible DamID System in Drosophila
A thorough study of the genome-wide binding patterns of chromatin proteins is essential for understanding the regulatory mechanisms of genomic processes in eukaryotic nuclei, including DNA replication, transcription, and repair. The DNA adenine methyltransferase identification (DamID) method is a powerful tool to identify genomic binding sites of chromatin proteins. This method does not require fixation of cells and the use of specific antibodies, and has been used to generate genome-wide binding maps of more than a hundred different proteins in Drosophila tissue culture cells. Recent versions of inducible DamID allow performing cell type-specific profiling of chromatin proteins even in small samples of Drosophila tissues that contain heterogeneous cell types. Importantly, with these methods sorting of cells of interest or their nuclei is not necessary as genomic DNA isolated from the whole tissue can be used as an input. Here, I describe in detail an FLP-inducible DamID method, namely generation of suitable transgenic flies, activation of the Dam transgenes by the FLP recombinase, isolation of DNA from small amounts of dissected tissues, and subsequent identification of the DNA binding sites of the chromatin proteins.
Key wordsDrosophila melanogaster Chromatin proteins Genomic binding sites DamID Cell type-specific profiling “Flp-Out” approach
I thank the laboratory of Prof. B. van Steensel at the Netherlands Cancer Institute (Amsterdam, the Netherlands) for providing an excellent working environment, the NKI Genomics Core Facility for help with the development of the protocol for preparation of DNA samples for Illumina high-throughput sequencing; Anna A. Ogienko for technical support; Mario Amendola, Maurizio Gatti, and the members of Laboratory of Cell Division for critical reading of the manuscript and helpful suggestions. This work was supported by the grant of Russian Science Foundation no. 16-14-10288.
- 26.Filion GJ, van Bemmel JG, Braunschweig U, Talhout W, Kind J, Ward LD, Brugman W, de Castro IJ, Kerkhoven RM, Bussemaker HJ, van Steensel B (2010) Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 143(2):212–224CrossRefPubMedPubMedCentralGoogle Scholar
- 27.Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Graf S, Flicek P, Kerkhoven RM, van Lohuizen M, Reinders M, Wessels L, van Steensel B (2010) Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell 38(4):603–613CrossRefPubMedGoogle Scholar
- 30.Kind J, Pagie L, de Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, de Graaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny LA, Jalink K, Dekker J, van Oudenaarden A, van Steensel B (2015) Genome-wide maps of nuclear lamina interactions in single human cells. Cell 163(1):134–147CrossRefPubMedPubMedCentralGoogle Scholar
- 32.Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczynski B, Riddell A, Furlong EE (2012) Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nat Genet 44(2):148–156CrossRefPubMedGoogle Scholar