KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-GFP | Thermo Fisher Scientific | Cat#A-11120; RRID:AB_221568 |
| Goat anti-mouse secondary antibody, Alexa Fluor Plus 488 | Thermo Fisher Scientific | Cat#A32723; RRID:AB_2633275 |
| Goat Anti-Rabbit IgG H&L (HRP) | Abcam | Cat#ab6721 RRID:AB_955447 |
| Rabbit polyclonal anti-H3K27ac | Abcam | Cat#ab4729; RRID:AB_2118291 |
| Rabbit polyclonal anti-H2A.Z | Abcam | Cat#ab4174; RRID:AB_304345 |
| Rabbit polyclonal anti-H2BK15ac | Diagenode | Cat#C15410220 |
| Rabbit polyclonal anti-H2AK5ac | Diagenode | Cat#C15410215; |
| Rabbit monoclonal anti-BRD4 | Cell Signaling Technology | Cat#13440; RRID:AB_2687578 |
| Rabbit monoclonal anti-H2A.Z(Lys4/Lys7)ac | Cell Signaling Technology | Cat#75336, RRID:AB_2799867 |
| Rabbit monoclonal anti-H2BK5ac | Cell Signaling Technology | Cat#12799; RRID:AB_2636805 |
| Rabbit monoclonal anti-H3K14ac | Cell Signaling Technology | Cat#7627; RRID:AB_10839410 |
| Rabbit monoclonal anti-H3K36ac | Cell Signaling Technology | Cat#27683; RRID:AB_2798946 |
| Rabbit monoclonal anti-H4K16ac | Cell Signaling Technology | Cat#13534; RRID:AB_2687581 |
| Rabbit polyclonal anti-H3K9ac | Active Motif | Cat#39137; RRID:AB_2561017 |
| Rabbit polyclonal anti-H3K18ac | Abcam | Cat#ab1191; AB_298692 |
| Rabbit polyclonal anti-H4K8ac | Abcam | Cat#ab15823; RRID:AB_880455 |
| Rabbit polyclonal anti-H3K4me3 | Abcam | Cat#ab8580 RRID:AB_306649 |
| Rabbit polyclonal anti-H3K4me1 | Diagenode | Cat#C15310037 |
| Mouse monoclonal anti-Pol II [8WG16] | Abcam | Cat#ab817; RRID:AB_306327 |
| Mouse monoclonal anti-Pol II [8WG16] | BioLegend | Cat#664912; RRID:AB_2650945 |
| Goat polyclonal anti-Myc tag | Abcam | Cat#ab9132; RRID:AB_307033 |
| Goat anti-rabbit-IgG-Atto647N | Sigma-Aldrich | Cat#40839; RRID:AB_1137669 |
| Rabbit polyclonal anti-Actin | Sigma-Aldrich | Cat#A5060; RRID:AB_476738 |
| Mouse monoclonal anti-FLAG | Sigma-Aldrich | Cat#F3165; RRID:AB_259529 |
| Rabbit polyclonal anti-p300a | This paper | N/A |
| Rabbit polyclonal anti-Nfya | Charles Sagerström lab | N/A |
| Rabbit polyclonal anti-Eomesa | Fiona Wardle lab | N/A |
| Rabbit polyclonal anti-Brd4 | Dawid lab | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| α-amanitin | Sigma-Aldrich | Cat#A2263 |
| Triptolide | Sigma-Aldrich | Cat#T3652 |
| Flavopiridol hydrochloride hydrate | Sigma-Aldrich | Cat# F3055 |
| Critical Commercial Assays | ||
| ChIP DNA Clean & Concentrator Kits | ZYMO RESEARCH | Cat#D5205 |
| Nextera DNA Library Prep Kit | Illumina | Cat#FC-121–1030 |
| Click-iT™ RNA Alexa Fluor™ 594 Imaging Kit | Thermo Fisher Scientific | Cat#C10330 |
| Click-iT™ Nascent RNA Capture Kit | Thermo Fisher Scientific | Cat#C10365 |
| SuperScript™ VILO™ cDNA Synthesis Kit | Thermo Fisher Scientific | Cat#11754–050 |
| MAXIscript™ SP6 Transcription Kit | Thermo Fisher Scientific | Cat#AM1308 |
| mMESSAGE mMACHINE™ T3 Transcription Kit | Thermo Fisher Scientific | Cat#AM1348 |
| mMESSAGE mMACHINE™ SP6 Transcription Kit | Thermo Fisher Scientific | Cat#AM1340 |
| AmpliScribe™ T7-Flash™ Transcription Kit | Lucigen | Cat#ASF3257 |
| Deposited Data | ||
| Datasets for Omni-ATAC seq, ChIP-seq, Click-iT-seq, RNA-seq, CUT&TAG in WT and MZnps embryos | This paper | SRP355652 |
| Nanog ChIP-seq datasets | Xu et al., 2012 | GSE34683 |
| ATAC-seq datasets at oblong and sphere stages | Pálfy et al., 2020 | GSE130944 |
| ATAC-seq datasets at oblong and dome stages | Liu et al., 2018 | GSE101779 |
| CAGE datasets at high/oblong/sphere/shield stages | Nepal et al., 2013 | SRA055273 |
| Ribosome profiling datasets at 2 hpf | Bazzini et al., 2014 | GSE53693 |
| Experimental Models: Organisms/Strains | ||
| Zebrafish: MZnps, triple maternal-zygotic mutant for nanog−/−;pou5f3−/−;sox19b−/− | This paper | N/A |
| Zebrafish: TU-AB, and TL strains | N/A | N/A |
| Oligonucleotides (See Table S1 for oligonucleotides used) | ||
| Recombinant DNA | ||
| pT3TS-zdCas9–3XGFP | Chan et al., 2019 | N/A |
| pcDNA-dCas9-p300 Core | Hilton et al., 2015 | Addgene Plasmid #61357; RRID:Addgene_61357 |
| pT3TS-dCas9-HAT | This paper | N/A |
| pT3TS-dCas9-dHAT | This paper | N/A |
| pCS2+nanog | Lee et al., 2013 | N/A |
| pCS2+pou5f3 | Lee et al., 2013 | N/A |
| pCS2+pou5f3–6Xmyc | This paper | N/A |
| pCS2+sox19b-6Xmyc | This paper | N/A |
| Software and Algorithms | ||
| Bowtie2 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2 |
| Skewer | Jiang et al., 2014 | https://github.com/relipmoc/skewer |
| STAR | Dobin et al., 2012 | https://github.com/alexdobin/STAR |
| SAMtools | Li et al., 2009 | http://www.htslib.org |
| BEDTools | Quinlan et al., 2010 | https://bedtools.readthedocs.io/en/latest/ |
| MACS2 | Zhang et al., 2008 | https://github.com/taoliu/MACS |
| DESeq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/ht ml/DESeq2.html |
| MEME suite | Bailey et al., 2009 | http://meme-suite.org |
| Nucleosome occupancy prediction model | Kaplan et al. 2009 | https://github.com/KaplanLab/NucleosomeModel |
| Python | Python 3.8 | https://www.python.org |
| R | R 3.6.2 | https://www.r-project.org |
| GeneAbacus | Charles E. Vejnar | https://github.com/vejnar/geneabacus |
| FONtools | Charles E. Vejnar | https://github.com/vejnar/fontools |
| LabxDB seq | Vejnar et al., 2020 | https://gitlab.com/vejnar/labxdb |