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Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing

Nature Structural & Molecular Biology volume 17, pages 894–900 (2010)Cite this article

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Abstract

Histone modifications are thought to regulate gene expression in part by modulating DNA accessibility. Here, we measured genome-wide DNA accessibility in Drosophila melanogaster by combining M.SssI methylation footprinting with methylated DNA immunoprecipitation. We show that methylase accessibility demarcates differential distribution of active and repressive histone modifications as well as sites of transcription and replication initiation. DNA accessibility is increased at active promoters and chromosomal regions that are hyperacetylated at H4K16, particularly at the male X chromosome, suggesting that transcriptional dosage compensation is facilitated by permissive chromatin structure. Conversely, inactive chromosomal domains decorated with H3K27me3 are least accessible, supporting a model for Polycomb-mediated chromatin compaction. In addition, we detect higher accessibility at chromosomal regions that replicate early and at sites of replication initiation. Together, these findings indicate that differential histone-modification patterns and the organization of replication have distinct and measurable effects on the exposure of the DNA template.

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Figure 1: Genome-wide chromatin-accessibility measurement using methylation footprinting.
Figure 2: Distribution of accessibility, transcription and chromatin marks across active genes.
Figure 3: Chromosomal regions of H3K27 trimethylation have reduced DNA accessibility.
Figure 4: Elevated accessibility of the dosage-compensated X chromosome.
Figure 5: Increased accessibility at sites of early replication.

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  • 04 July 2010

    In the version of this article initially published online, a comma was missing from the title. The error has been corrected for the print, PDF and HTML versions of this article.

References

  1. McGhee, J.D., Wood, W.I., Dolan, M., Engel, J.D. & Felsenfeld, G. A 200 base pair region at the 5′ end of the chicken adult β-globin gene is accessible to nuclease digestion. Cell 27, 45–55 (1981).

    Article  CAS  Google Scholar 

  2. Wu, C., Wong, Y.C. & Elgin, S.C. The chromatin structure of specific genes: II. Disruption of chromatin structure during gene activity. Cell 16, 807–814 (1979).

    Article  CAS  Google Scholar 

  3. Weintraub, H. & Groudine, M. Chromosomal subunits in active genes have an altered conformation. Science 193, 848–856 (1976).

    Article  CAS  Google Scholar 

  4. Boivin, A. & Dura, J.M. In vivo chromatin accessibility correlates with gene silencing in Drosophila. Genetics 150, 1539–1549 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Fatemi, M. et al. Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level. Nucleic Acids Res. 33, e176 (2005).

    Article  Google Scholar 

  6. Gottschling, D.E. Telomere-proximal DNA in Saccharomyces cerevisiae is refractory to methyltransferase activity in vivo. Proc. Natl. Acad. Sci. USA 89, 4062–4065 (1992).

    Article  CAS  Google Scholar 

  7. Singh, J. & Klar, A.J. Active genes in budding yeast display enhanced in vivo accessibility to foreign DNA methylases: a novel in vivo probe for chromatin structure of yeast. Genes Dev. 6, 186–196 (1992).

    Article  CAS  Google Scholar 

  8. Felsenfeld, G. & Groudine, M. Controlling the double helix. Nature 421, 448–453 (2003).

    Article  Google Scholar 

  9. Pokholok, D.K. et al. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122, 517–527 (2005).

    Article  CAS  Google Scholar 

  10. Schubeler, D. et al. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev. 18, 1263–1271 (2004).

    Article  Google Scholar 

  11. Lee, C.K., Shibata, Y., Rao, B., Strahl, B.D. & Lieb, J.D. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat. Genet. 36, 900–905 (2004).

    Article  CAS  Google Scholar 

  12. Schones, D.E. et al. Dynamic regulation of nucleosome positioning in the human genome. Cell 132, 887–898 (2008).

    Article  CAS  Google Scholar 

  13. Boyle, A.P. et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132, 311–322 (2008).

    Article  CAS  Google Scholar 

  14. Sabo, P.J. et al. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat. Methods 3, 511–518 (2006).

    Article  CAS  Google Scholar 

  15. Shogren-Knaak, M. et al. Histone H4–K16 acetylation controls chromatin structure and protein interactions. Science 311, 844–847 (2006).

    Article  CAS  Google Scholar 

  16. Akhtar, A. & Becker, P.B. Activation of transcription through histone H4 acetylation by MOF, an acetyltransferase essential for dosage compensation in Drosophila. Mol. Cell 5, 367–375 (2000).

    Article  CAS  Google Scholar 

  17. Bone, J.R. et al. Acetylated histone H4 on the male X chromosome is associated with dosage compensation in Drosophila. Genes Dev. 8, 96–104 (1994).

    Article  CAS  Google Scholar 

  18. Smith, E.R. et al. The Drosophila MSL complex acetylates histone H4 at lysine 16, a chromatin modification linked to dosage compensation. Mol. Cell. Biol. 20, 312–318 (2000).

    Article  CAS  Google Scholar 

  19. Schotta, G. et al. Central role of Drosophila SU(VAR)3–9 in histone H3–K9 methylation and heterochromatic gene silencing. EMBO J. 21, 1121–1131 (2002).

    Article  CAS  Google Scholar 

  20. Peters, A.H. et al. Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell 107, 323–337 (2001).

    Article  CAS  Google Scholar 

  21. Bannister, A.J. et al. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410, 120–124 (2001).

    Article  CAS  Google Scholar 

  22. Lachner, M., O'Carroll, D., Rea, S., Mechtler, K. & Jenuwein, T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410, 116–120 (2001).

    Article  CAS  Google Scholar 

  23. Cao, R. et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039–1043 (2002).

    Article  CAS  Google Scholar 

  24. Francis, N.J., Kingston, R.E. & Woodcock, C.L. Chromatin compaction by a polycomb group protein complex. Science 306, 1574–1577 (2004).

    Article  CAS  Google Scholar 

  25. Lanzuolo, C., Roure, V., Dekker, J., Bantignies, F. & Orlando, V. Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nat. Cell Biol. 9, 1167–1174 (2007).

    Article  CAS  Google Scholar 

  26. Tiwari, V.K., Cope, L., McGarvey, K.M., Ohm, J.E. & Baylin, S.B. A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations. Genome Res. 18, 1171–1179 (2008).

    Article  CAS  Google Scholar 

  27. Weber, M. et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 37, 853–862 (2005).

    Article  CAS  Google Scholar 

  28. Mito, Y., Henikoff, J.G. & Henikoff, S. Histone replacement marks the boundaries of cis-regulatory domains. Science 315, 1408–1411 (2007).

    Article  CAS  Google Scholar 

  29. Schwaiger, M. et al. Chromatin state marks cell-type- and gender-specific replication of the Drosophila genome. Genes Dev. 23, 589–601 (2009).

    Article  CAS  Google Scholar 

  30. Schwartz, Y.B. et al. Genome-wide analysis of Polycomb targets in Drosophila melanogaster. Nat. Genet. 38, 700–705 (2006).

    Article  CAS  Google Scholar 

  31. Shimizu, T.S., Takahashi, K. & Tomita, M. CpG distribution patterns in methylated and non-methylated species. Gene 205, 103–107 (1997).

    Article  CAS  Google Scholar 

  32. Lyko, F. et al. Mammalian (cytosine-5) methyltransferases cause genomic DNA methylation and lethality in Drosophila. Nat. Genet. 23, 363–366 (1999).

    Article  CAS  Google Scholar 

  33. Wirbelauer, C., Bell, O. & Schubeler, D. Variant histone H3.3 is deposited at sites of nucleosomal displacement throughout transcribed genes while active histone modifications show a promoter-proximal bias. Genes Dev. 19, 1761–1766 (2005).

    Article  CAS  Google Scholar 

  34. Bell, O. et al. Localized H3K36 methylation states define histone H4K16 acetylation during transcriptional elongation in Drosophila. EMBO J. 26, 4974–4984 (2007).

    Article  CAS  Google Scholar 

  35. Carrozza, M.J. et al. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123, 581–592 (2005).

    Article  CAS  Google Scholar 

  36. Keogh, M.C. et al. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123, 593–605 (2005).

    Article  CAS  Google Scholar 

  37. King, I.F., Francis, N.J. & Kingston, R.E. Native and recombinant polycomb group complexes establish a selective block to template accessibility to repress transcription in vitro. Mol. Cell. Biol. 22, 7919–7928 (2002).

    Article  CAS  Google Scholar 

  38. Shao, Z. et al. Stabilization of chromatin structure by PRC1, a Polycomb complex. Cell 98, 37–46 (1999).

    Article  CAS  Google Scholar 

  39. Fitzgerald, D.P. & Bender, W. Polycomb group repression reduces DNA accessibility. Mol. Cell. Biol. 21, 6585–6597 (2001).

    Article  CAS  Google Scholar 

  40. Zink, D. & Paro, R. Drosophila Polycomb-group regulated chromatin inhibits the accessibility of a trans-activator to its target DNA. EMBO J. 14, 5660–5671 (1995).

    Article  CAS  Google Scholar 

  41. Dellino, G.I. et al. Polycomb silencing blocks transcription initiation. Mol. Cell 13, 887–893 (2004).

    Article  CAS  Google Scholar 

  42. Stock, J.K. et al. Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells. Nat. Cell Biol. 9, 1428–1435 (2007).

    Article  CAS  Google Scholar 

  43. Turner, B.M., Birley, A.J. & Lavender, J. Histone H4 isoforms acetylated at specific lysine residues define individual chromosomes and chromatin domains in Drosophila polytene nuclei. Cell 69, 375–384 (1992).

    Article  CAS  Google Scholar 

  44. Bell, O. et al. Transcription-coupled methylation of histone H3 at lysine 36 regulates dosage compensation by enhancing recruitment of the MSL complex in Drosophila melanogaster. Mol. Cell. Biol. 28, 3401–3409 (2008).

    Article  CAS  Google Scholar 

  45. Corona, D.F., Clapier, C.R., Becker, P.B. & Tamkun, J.W. Modulation of ISWI function by site-specific histone acetylation. EMBO Rep. 3, 242–247 (2002).

    Article  CAS  Google Scholar 

  46. Gilfillan, G.D. et al. Chromosome-wide gene-specific targeting of the Drosophila dosage compensation complex. Genes Dev. 20, 858–870 (2006).

    Article  CAS  Google Scholar 

  47. Hiratani, I., Takebayashi, S., Lu, J. & Gilbert, D.M. Replication timing and transcriptional control: beyond cause and effect—part II. Curr. Opin. Genet. Dev. 19, 142–149 (2009).

    Article  CAS  Google Scholar 

  48. Hansen, K.H. et al. A model for transmission of the H3K27me3 epigenetic mark. Nat. Cell Biol. 10, 1291–1300 (2008).

    Article  CAS  Google Scholar 

  49. Mendjan, S. et al. Nuclear pore components are involved in the transcriptional regulation of dosage compensation in Drosophila. Mol. Cell 21, 811–823 (2006).

    Article  CAS  Google Scholar 

  50. Aggarwal, B.D. & Calvi, B.R. Chromatin regulates origin activity in Drosophila follicle cells. Nature 430, 372–376 (2004).

    Article  CAS  Google Scholar 

  51. Knott, S.R., Viggiani, C.J., Tavare, S. & Aparicio, O.M. Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae. Genes Dev. 23, 1077–1090 (2009).

    Article  CAS  Google Scholar 

  52. Vogelauer, M., Rubbi, L., Lucas, I., Brewer, B.J. & Grunstein, M. Histone acetylation regulates the time of replication origin firing. Mol. Cell 10, 1223–1233 (2002).

    Article  CAS  Google Scholar 

  53. MacAlpine, D.M. & Bell, S.P. A genomic view of eukaryotic DNA replication. Chromosome Res. 13, 309–326 (2005).

    Article  CAS  Google Scholar 

  54. Sequeira-Mendes, J. et al. Transcription initiation activity sets replication origin efficiency in mammalian cells. PLoS Genet. 5, e1000446 (2009).

    Article  Google Scholar 

  55. Beisel, C. et al. Comparing active and repressed expression states of genes controlled by the Polycomb/Trithorax group proteins. Proc. Natl. Acad. Sci. USA 104, 16615–16620 (2007).

    Article  CAS  Google Scholar 

  56. Strutt, H. & Paro, R. The polycomb group protein complex of Drosophila melanogaster has different compositions at different target genes. Mol. Cell. Biol. 17, 6773–6783 (1997).

    Article  CAS  Google Scholar 

  57. Schubeler, D., Lorincz, M.C. & Groudine, M. Targeting silence: the use of site-specific recombination to introduce in vitro methylated DNA into the genome. Sci. STKE 2001, pl1 (2001).

    CAS  PubMed  Google Scholar 

  58. Edgar, R., Domrachev, M. & Lash, A.E. Gene Expression Omnibus: NCBI gene expression a hybridization array data repository. Nucleic Acids Res. 30, 201–210 (2002).

    Article  Google Scholar 

  59. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

    Article  Google Scholar 

  60. Koenker, R. quantreg: Quantile Regression. R package version 4.36 (2009) <http://www.r-project.org>.

  61. The R Development Core Team. R: A Language and Environment for Statistical Computing version 2.11.0 (Vienna, Austria, 2006).

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Acknowledgements

We thank S. Gasser, L. Ho, G.R. Crabtree and members of our laboratory for helpful comments on the manuscript, H. Angliker for Affymetrix microarray processing, D. Gaidatzis for codeveloping of the deep sequencing analysis software and I. Nissen for sample processing for deep sequencing. Illumina sequencing was carried out at the Laboratory of Quantitative Genomics, D-BSSE. O.B. and M.S. are supported by European Molecular Biology Organization long-term fellowships, M.S. and F.L. acknowledge support by a predoctoral fellowship of the Boehringer Ingelheim Fonds. Research in the laboratory of D.S. is supported by the Novartis Research Foundation, by the European Union (NoE “The Epigenome” LSHG-CT-2004-503433, LSHG-CT-2006-037415), the European Research Council (ERC-204264) and the European Molecular Biology Organization Young Investigator program.

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  1. Oliver Bell, Michaela Schwaiger & Edward J Oakeley

    Present address: Present addresses: Howard Hughes Medical Institute and the Department of Pathology, Stanford University, Stanford, California, USA (O.B.), Department for Molecular Evolution and Development, Centre for Organismal Systems Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria (M.S.) and Novartis Institutes for BioMedical Research, BMD/Genome Technologies and Novartis Pharma AG, Basel, Switzerland (E.J.O.).,

  2. Oliver Bell and Michaela Schwaiger: These authors contributed equally to this work.

Authors and Affiliations

  1. Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland

    Oliver Bell, Michaela Schwaiger, Edward J Oakeley, Florian Lienert, Michael B Stadler & Dirk Schübeler

  2. Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland

    Christian Beisel

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Contributions

O.B. and M.S. performed ChIP and MeDIP footprinting experiments; E.J.O. supervised microarray experiments; M.S. and M.B.S. performed all bioinformatics analyses; O.B. and F.L. performed bisulfite sequencing; C.B. carried out Psc ChIP and Illumina sequencing; D.S. supervised the analyses; O.B., M.S. and D.S. prepared the manuscript in consultation with all coauthors.

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Correspondence to Dirk Schübeler.

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Bell, O., Schwaiger, M., Oakeley, E. et al. Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing. Nat Struct Mol Biol 17, 894–900 (2010). https://doi.org/10.1038/nsmb.1825

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