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Genome-wide analysis of Polycomb targets in Drosophila melanogaster

Nature Genetics volume 38, pages 700–705 (2006)Cite this article

Abstract

Polycomb group (PcG) complexes are multiprotein assemblages that bind to chromatin and establish chromatin states leading to epigenetic silencing1,2. PcG proteins regulate homeotic genes in flies and vertebrates, but little is known about other PcG targets and the role of the PcG in development, differentiation and disease. Here, we determined the distribution of the PcG proteins PC, E(Z) and PSC and of trimethylation of histone H3 Lys27 (me3K27) in the D. melanogaster genome. At more than 200 PcG target genes, binding sites for the three PcG proteins colocalize to presumptive Polycomb response elements (PREs). In contrast, H3 me3K27 forms broad domains including the entire transcription unit and regulatory regions. PcG targets are highly enriched in genes encoding transcription factors, but they also include genes coding for receptors, signaling proteins, morphogens and regulators representing all major developmental pathways.

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Figure 1: Distribution of PcG proteins and H3 me3K27 mark on chromosome 3R.
Figure 2: PcG and me3K27 profile at the Bithorax complex.
Figure 3: PC and me3K27 bind to much broader regions than PSC or E(Z).
Figure 4: Profiles of me3K27 and PcG proteins at representative PcG sites.
Figure 5: NK homeodomain cluster and dco-Sox10B0 site.
Figure 6: Genes encoding regulators of transcription are greatly enriched among PcG targets.

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Acknowledgements

We are grateful to T. Jenuwein for the anti-H3 me3K27 antibody; to D. McCabe for polytene chromosome preparations; to A. Brooks, Q. Wang and V. Patel of the Bionomics Research and Technology Center of the Rutgers Environmental and Occupational Health Sciences Institute for hybridization and scanning of the microarrays. Particular thanks to M. Eisen for leading the Berkeley Drosophila Transcription Network Project's development of ChIP/chip data analysis methods and for encouraging this work. Work conducted by the BDTNP is funded by a grant from the US National Institute of General Medical Sciences and the US National Human Genome Research Institute (GM704403) at Lawrence Berkeley National Laboratory under Department of Energy contract DE-AC02-05CH11231.

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Authors and Affiliations

  1. Department of Molecular Biology and Biochemistry, Rutgers University, 604 Allison Road, Piscataway, 08854, New Jersey, USA

    Yuri B Schwartz, Tatyana G Kahn & Vincenzo Pirrotta

  2. Genomics Division, Berkeley Drosophila Transcription Network Project, Lawrence Berkeley National Laboratory, Berkeley, 94720, California, USA

    David A Nix, Xiao-Yong Li & Mark Biggin

  3. Department of Statistics, University of California, Berkeley, Berkeley, 94720, California, USA

    Richard Bourgon

  4. Affymetrix, 6550 Vallejo Street, Emeryville, 94608, California, USA

    David A Nix

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  1. Yuri B Schwartz
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Correspondence to Vincenzo Pirrotta.

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D.A.N. is employed by Affymetrix.

Supplementary information

Supplementary Fig. 1

Distribution of PcG proteins and H3 me3K27 mark along the X chromosome. (PDF 81 kb)

Supplementary Fig. 2

Distribution of PcG proteins and H3 me3K27 mark along chromosome 4. (PDF 84 kb)

Supplementary Fig. 3

Distribution of PcG proteins and H3 me3K27 mark along 2L chromosome. (PDF 83 kb)

Supplementary Fig. 4

Distribution of PcG proteins and H3 me3K27 mark along 2R chromosome. (PDF 81 kb)

Supplementary Fig. 5

Distribution of PcG proteins and H3 me3K27 mark along 3L chromosome. (PDF 82 kb)

Supplementary Fig. 6

Co-localization between the binding of PSC and other PcG proteins. (PDF 44 kb)

Supplementary Fig. 7

Co-localization between the binding of E(Z) and other PcG proteins. (PDF 42 kb)

Supplementary Fig. 8

Comparison of microarray data to the Ringrose et al. genome-wide prediction of PREs. (PDF 21 kb)

Supplementary Fig. 9

PcG proteins bind to ph and Psc-Su(z)2 polycomb group genes. (PDF 129 kb)

Supplementary Fig. 10

Valication of microarray hybridization results by real-time PCR. (PDF 207 kb)

Supplementary Table 1

List of PcG sites. (PDF 196 kb)

Supplementary Table 2

General features of PcG sites. (PDF 53 kb)

Supplementary Table 3

List of PCR primers. (PDF 69 kb)

Supplementary Methods (PDF 62 kb)

Supplementary Note (PDF 12 kb)

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Schwartz, Y., Kahn, T., Nix, D. et al. Genome-wide analysis of Polycomb targets in Drosophila melanogaster. Nat Genet 38, 700–705 (2006). https://doi.org/10.1038/ng1817

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