Science Advances

Supplementary Materials

The PDF set includes:

  • Fig. S1. Resolution of Hi-C maps.
  • Fig. S2. SOMs of 10 PTM ChIP-seq from ED.
  • Fig. S3. aTSS and aTSS SOM clusters are transcriptionally active.
  • Fig. S4. A subset of active enhancers shows substantial H2AK118Ub enrichment in the ED.
  • Fig. S5. High levels of PRC1 and H2AK118Ub are associated with increased enhancer-promoter interaction frequencies at short-range distances (25 to 250 kb).
  • Fig. S6. High levels of PRC1 are associated with increased enhancer-promoter interaction frequencies at long-range distances (250 kb to 5 Mb).
  • Fig. S7. Quantification of PTM ChIP-seq signal for each cluster of PRC1 peaks.
  • Fig. S8. PRC1 clusters have distinct genomic features.
  • Fig. S9. k-Means clustering of ED ATAC-seq peaks provides control sets of aTSSs and enhancers.
  • Fig. S10. PRC1-bound aTSSs form loops with the TTS of the corresponding genes, whereas PRC1-bound enhancers do not.
  • Fig. S11. PRC1 binding is associated with increased aTSS-aTSS and enhancer-enhancer contact frequencies in ED.
  • Fig. S12. PRC1 redeployment at a subset of SSEs coincides with increased enhancer marks and enhancer-promoter contacts at the larval stage.
  • Fig. S13. UAS-ph RNAi clones phenocopy ph mutant clones.
  • Fig. S14. The transcriptional response to ph depletion varies upon chromatin types.
  • Fig. S15. Canonical Polycomb sites enriched for H2AK118Ub show higher H3K4me1 levels and higher contact frequencies in ED.
  • Fig. S16. Removal of the two PRC1 anchors at the dac locus dampens its expression, while its expression pattern remains unchanged.
  • Fig. S17. RING1B is redeployed at active enhancer sites in NPCs.
  • Fig. S18. Clustering of ChIP-seq and Hi-C replicates from ED and whole Drosophila embryos.

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Chromatin types from Drosophila ED.
  • Table S2 (Microsoft Excel format). Gene ontologies of the top interacting aTSS bins identified on the basis of PH ChIP-seq enrichment.
  • Table S3 (Microsoft Excel format). Stringent set of PRC1 peak summits used for the clustering in ED.
  • Table S4 (Microsoft Excel format). List of the genes assigned to each cluster of PRC1 peaks in ED.
  • Table S5 (Microsoft Excel format). FPKM of Drosophila genes for the different conditions used in this study.
  • Table S6 (Microsoft Excel format). Comparative Gene Ontology analysis of the genes assigned to each cluster of PRC1 peaks in ED.
  • Table S7 (Microsoft Excel format). Differential gene expression analyses during development and in polycomb mutant Eds.
  • Table S8 (Microsoft Excel format). List of the antibodies used in the study.
  • Table S9 (Microsoft Excel format). PCR primers used in the study.
  • Table S10 (Microsoft Excel format). NGS datasets used in the study.

Files in this Data Supplement: