Nucleation-dependent propagation of Polycomb modifications emerges during the Drosophila maternal to zygotic transition

The manuscript associated with these datasets seeks to address the timing of acquisition of chromatin modifications associated with Polycomb group (PcG) function during the maternal-to-zygotic transition of Drosophila melanogaster. PcG modifications including mono- and tri-methylation of Histone H3 at Lysine 27 (H3K27me1, me3) and ubiquitylation of H2A at lysine 118 (H2Aub) were measured by ChIP-seq in precisely staged embryo collections spanning large scale zygotic genome activation (ZGA), over nuclear divisions NC13 and three timepoints in NC14 (NC14-early, -mid, and -late). Additionally, marks associated with active transcription, including mono- di- and tri-methylation of Histone H3 at Lysine 4 (H3K4me1, me2, me3), RNA Pol2 phosphorylated at serine 5 of the C-terminal domain heptapeptide repeats, and acetylation of Histone H3 at Lysine 27 (H3K27ac) were measured at NC14. We additionally measured genomic localization of the H3K27me3 methyltransferase, Enhancer of zeste (E(z)), and of three factors known to bind Polycomb Response Elements, Pho, Combgap, and GAGA-Factor (GAF), by generating GFP chimeras to these proteins using CRISPR/Cas9 and performing ChIP against the GFP tagged proteins. Data for these GFP-ChIP-seq localization experiments is from embryos collected during NC14. To test for the contribution of DNA binding factors to the establishment of PcG modifications, we additionally measured deposition of H3K27me3 in embryos where GAF was sequestered from nuclei using Jabba Trap (JT-GAF), and measured H3K27me3, H2Aub, E(z), and RNA Pol2 in embryos from zelda mutant germline clones staged at mid-NC14. Negative control ChIP-seq datasets are provided in the form of anti-GFP ChIP in wild-type embryos that express no GFP tagged protein. The samples deposited here break down into three general experimental groups. 1) Developmental Timecourse Data for wild-type embryos staged from NC13 through three timepoints of NC14 (E = early, M = mid, L = late), for H3K27me1, H3K27me3, and H2Aub. These experiments are supported as well by measurements for H3K4me1, H3K4me2, H3K4me3, RNAPol2, and H3K27ac measurements collected only at NC14. 2) Localization experiments for GFP-tagged E(z), Pho, Cg, and GAF, all staged at NC14. 3) Measurement of GAF localization and H3K27me3 deposition comparing GFP-GAF and Jabba-trap sequestered GFP-GAF (JT-GAF). 4) Measurement of H3K27me3, H2Aub, RNA Pol2, and E(z) localization in zelda germline clone embryos staged at mid-NC14. The negative control experiment is a ChIP using the anti-GFP antibody in wild-type embryos. Data are provided as original paired-end FastQ files (PE75 or PE150). Peaks lists for E(z), Pho, GAF, and Cg, plus computed Polycomb Domains are provided as well as counts-per-million normalized coverage plots (bigwig) for merged replicates for all key comparisons. Two or more independent biological replicates were measured for each condition. Several genotypes represent wild-type embryos in this study. For the negative control experiment, w[1118] embryos were used. Fluorescent markers were included to help stage embryos, and these are otherwise wild-type strains. The fluorescent markers are RpA70-EGFP and His2Av-RFP. RpA-70-EGFP was favored in all cases except when the desired ChIP target was also EGFP tagged, in which case His2Av-RFP was used instead.