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Chromatin profiling using targeted DNA adenine methyltransferase

Abstract

Chromatin is the highly complex structure consisting of DNA and hundreds of associated proteins. Most chromatin proteins exert their regulatory and structural functions by binding to specific chromosomal loci. Knowledge of the identity of these in vivo target loci is essential for the understanding of the functions and mechanisms of action of chromatin proteins. We report here large-scale mapping of in vivo binding sites of chromatin proteins, using a novel approach based on a combination of targeted DNA methylation and microarray technology. We show that three distinct chromatin proteins in Drosophila melanogaster cells each associate with specific sets of genes. HP1 binds predominantly to pericentric genes and transposable elements. GAGA factor associates with euchromatic genes that are enriched in (GA)n motifs. A Drosophila homolog of Saccharomyces cerevisiae Sir2p is associated with several active genes and is excluded from heterochromatin. High-resolution, genome-wide maps of target loci of chromatin proteins ('chromatin profiles') provide new insights into chromatin structure and gene regulation.

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Figure 1: Experimental procedure for identifying in vivo targets of chromatin proteins.
Figure 2: Mapping of HP1 target loci.
Figure 3: Mapping of GAF target loci.
Figure 4: Mapping of Sir2 target loci.
Figure 5: Pair-wise comparison of binding patterns of HP1 and Sir2.

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References

  1. van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nature Biotechnol. 18, 424–428 (2000).

    Article  CAS  Google Scholar 

  2. James, T.C. et al. Distribution patterns of HP1, a heterochromatin-associated nonhistone chromosomal protein of Drosophila. Eur. J. Cell Biol. 50, 170–180 (1989).

    CAS  PubMed  Google Scholar 

  3. Pollack, J.R. et al. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nature Genet. 23, 41–46 (1999).

    Article  CAS  Google Scholar 

  4. Charlesworth, B., Jarne, P. & Assimacopoulos, S. The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. III Element abundances in heterochromatin. Genet. Res. 64, 183–197 (1994).

    Article  CAS  Google Scholar 

  5. Pimpinelli, S. et al. Transposable elements are stable structural components of Drosophila melanogaster heterochromatin. Proc. Natl. Acad. Sci. USA 92, 3804–3808 (1995).

    Article  CAS  Google Scholar 

  6. Carmena, M. & Gonzalez, C. Transposable elements map in a conserved pattern of distribution extending from β-heterochromatin to centromeres in Drosophila melanogaster. Chromosoma 103, 676–684 (1995).

    Article  CAS  Google Scholar 

  7. Henikoff, S. Heterochromatin function in complex genomes. Biochim. Biophys. Acta 1470, O1–O8 (1999).

    Google Scholar 

  8. Tsukiyama, T., Becker, P.B. & Wu, C. ATP-dependent nucleosome disruption at a heat-shock promoter mediated by binding of GAGA transcription factor. Nature 367, 525–532 (1994).

    Article  CAS  Google Scholar 

  9. Benyajati, C. et al. Multiple isoforms of GAGA factor, a critical component of chromatin structure. Nucleic Acids Res. 25, 3345–3353 (1997).

    Article  CAS  Google Scholar 

  10. Biggin, M.D. & Tjian, R. Transcription factors that activate the Ultrabithorax promoter in developmentally staged extracts. Cell 53, 699–711 (1988).

    Article  CAS  Google Scholar 

  11. Soeller, W.C., Oh, C.E. & Kornberg, T.B. Isolation of cDNAs encoding the Drosophila GAGA transcription factor. Mol. Cell. Biol. 13, 7961–7970 (1993).

    Article  CAS  Google Scholar 

  12. Strutt, H., Cavalli, G. & Paro, R. Co-localization of Polycomb protein and GAGA factor on regulatory elements responsible for the maintenance of homeotic gene expression. EMBO J. 16, 3621–3632 (1997).

    Article  CAS  Google Scholar 

  13. O'Brien, T., Wilkins, R.C., Giardina, C. & Lis, J.T. Distribution of GAGA protein on Drosophila genes in vivo. Genes Dev. 9, 1098–1110 (1995).

    Article  CAS  Google Scholar 

  14. Guarente, L. Sir2 links chromatin silencing, metabolism, and aging. Genes Dev. 14, 1021–1026 (2000).

    CAS  PubMed  Google Scholar 

  15. Gartenberg, M.R. The Sir proteins of Saccharomyces cerevisiae: mediators of transcriptional silencing and much more. Curr. Opin. Microbiol. 3, 132–137 (2000).

    Article  CAS  Google Scholar 

  16. Gotta, M. et al. Localization of Sir2p: the nucleolus as a compartment for silent information regulators. EMBO J. 16, 3243–3255 (1997).

    Article  CAS  Google Scholar 

  17. Cuperus, G., Shafaatian, R. & Shore, D. Locus specificity determinants in the multifunctional yeast silencing protein Sir2. EMBO J. 19, 2641–2651 (2000).

    Article  CAS  Google Scholar 

  18. Cockell, M.M., Perrod, S. & Gasser, S.M. Analysis of Sir2p domains required for rDNA and telomeric silencing in Saccharomyces cerevisiae. Genetics 154, 1069–1083 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Frye, R.A. Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem. Biophys. Res. Commun. 273, 793–798 (2000).

    Article  CAS  Google Scholar 

  20. Blat, Y. & Kleckner, N. Cohesins bind to preferential sites along yeast chromosome III, with differential regulation along arms versus the centric region. Cell 98, 249–259 (1999).

    Article  CAS  Google Scholar 

  21. Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306–2309 (2001).

    Article  Google Scholar 

  22. Iyer, V.R. et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409, 533–538 (2001).

    Article  CAS  Google Scholar 

  23. Wines, D.R., Talbert, P.B., Clark, D.V. & Henikoff, S. Introduction of a DNA methyltransferase into Drosophila to probe chromatin structure in vivo. Chromosoma 104, 332–340 (1996).

    Article  CAS  Google Scholar 

  24. Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc. Natl. Acad. Sci. USA 97, 716–721 (2000).

    Article  CAS  Google Scholar 

  25. de Lange, T. et al. Structure and variability of human chromosome ends. Mol. Cell. Biol. 10, 518–827 (1990).

    Article  CAS  Google Scholar 

  26. Kopczynski, C.C. et al. A high throughput screen to identify secreted and transmembrane proteins involved in Drosophila embryogenesis. Proc. Natl. Acad. Sci. USA 95, 9973–9978 (1998).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank E. Giniger for coordinating the assembly of the Northwest Fly Consortium microarray; C. Neal for help with microarray construction and analysis; P. Ng for help with the EST annotation; J. Smothers for the anti-HP1 antibody; J. O'Brien for technical assistance; and members of the Henikoff lab for suggestions.

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Correspondence to Bas van Steensel.

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van Steensel, B., Delrow, J. & Henikoff, S. Chromatin profiling using targeted DNA adenine methyltransferase. Nat Genet 27, 304–308 (2001). https://doi.org/10.1038/85871

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