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Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase

Abstract

We have developed a novel technique, named DamID, for the identification of DNA loci that interact in vivo with specific nuclear proteins in eukaryotes. By tethering Escherichia coli DNA adenine methyltransferase (Dam) to a chromatin protein, Dam can be targeted in vivo to native binding sites of this protein, resulting in local DNA methylation. Sites of methylation can subsequently be mapped using methylation-specific restriction enzymes or antibodies. We demonstrate the successful application of DamID both in Drosophila cell cultures and in whole flies. When Dam is tethered to the DNA-binding domain of GAL4, targeted methylation is limited to a region of a few kilobases surrounding a GAL4 binding sequence. Using DamID, we identified a number of expected and unexpected target loci for Drosophila heterochromatin protein 1. DamID has potential for genome-wide mapping of in vivo targets of chromatin proteins in various eukaryotes.

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Figure 1: Targeting of Dam to a specific sequence.
Figure 2: In situ detection of targeted methylation by Dam-HP1.
Figure 3: HP1-targeted methylation of specific genomic loci.

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Acknowledgements

We thank Dr. R. Lührmann for providing anti-m6A-antibody; S. Elgin for anti-HP1 antibody; Joel Eissenberg and Susan Parkhurst for plasmids; Keith Kerkof for TaqMan PCR advice; Kami Ahmad for help with microinjection and fly genetics and for suggesting the DamID name; Jorja Henikoff for help with statistical analysis; Peter Kim and Judith O'Brien for technical assistance; and members of our lab for unlimited enthusiasm and helpful suggestions.

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Correspondence to Bas van Steensel.

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Steensel, B., Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase. Nat Biotechnol 18, 424–428 (2000). https://doi.org/10.1038/74487

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