KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-Supt7l | Bethyl Laboratories | Cat#A302–803A; RRID:AB_10630265 |
| Mouse monoclonal anti-γTubulin | Sigma-Aldrich | Cat#T6557; RRID:AB_477584 |
| Rabbit polyclonal anti-Rpl29 | ThermoFisher Scientific | Cat#15799–1-AP; RRID:AB_2878187 |
| Rabbit polyclonal anti-histone H3 lysine 9 acetylation | Abcam | Cat#ab4441; RRID:AB_2118292 |
| Rabbit polyclonal anti-HA tag | Abcam | Cat#ab9110; RRID:AB_307019 |
| Mouse monoclonal anti-Wdr5 | Abcam | Cat#ab56919; RRID:AB_946146 |
| Mouse monoclonal anti-Tbp | In-house | 3TF1–3G3; Brou et al., 1993 |
| Rabbit polyclonal anti-Taf7 | In-house | 3475; Bardot et al., 2017 |
| Mouse monoclonal anti-Taf10 | In-house | 6TA-2B11; Jacq et al., 1994 |
| Mouse monoclonal anti-Taf12 | In-house | 22TA-2A1; Mengus et al., 1995 |
| Rabbit polyclonal anti-Atxn7l3 | In-house | 2325; Zhao et al., 2008 |
| Rabbit polyclonal anti-Supt3h | In-house | 3118; Bardot et al., 2017 |
| Rabbit polyclonal anti-Gcn5 | In-house | 2676; Nagy et al., 2010; Orpinell et al., 2010 |
| Mouse monoclonal anti-Gcn5 | In-house | 2GC-2C11; Brand et al., 2001 |
| Rabbit polyclonal anti-Tada3 | In-house | 2678; Nagy et al., 2010; Orpinell et al., 2010 |
| Rabbit polyclonal anti-Sgf29 | In-house | 2461; Orpinell et al., 2010 |
| Rabbit polyclonal anti-Atac2 | In-house | 2734; Nagy et al., 2010 |
| Rabbit polyclonal anti-Mbip | In-house | 2768; Nagy et al., 2010; Orpinell et al., 2010 |
| Rabbit polyclonal anti-Zzz3 | In-house | 2616; Nagy et al., 2010 |
| Chemicals, peptides, and recombinant proteins | ||
| Indole-3-acetic acid | Sigma-Aldrich | Cat#I3750 |
| 4-thiouridine | Glentham Life Sciences or abcam | Cat#GN6085 or Cat#ab143718 |
| 4-thiouracil | Sigma-Aldrich | Cat#440736 |
| EZ-link HPDP-biotin | ThermoFisher Scientific | Cat#21341 |
| Streptavidin protein coupled to HRP | ThermoFisher Scientific | Cat#21126 |
| Home-made Tn5E54K,L372P transposase | Plasmid provided by Dr. Kim Remans, EMBL Heidelberg, Germany | Hennig et al., 2018 |
| Critical commercial assays | ||
| Alkaline Phosphatase Kit | Vector Laboratories | Cat#SK-5100 |
| TURBO DNA-free™ Kit | ThermoFisher Scientific | Cat#AM1907 |
| μMACS magnetic beads and columns | Miltenyi Biotec | Cat#130–074–101 |
| RNeasy MinElute Cleanup Kit | QIAGEN | Cat#74204 |
| NucleoSpin Gel and PCR Clean-up kit | Macherey-Nagel | Cat#740609.50 |
| RiboPure™ RNA Purification Kit | ThermoFisher Scientific | Cat#AM1926 |
| TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo-Zero Gold | Illumina | Cat#RS-122–2301 or Cat#RS-122–2302 |
| Ribo-Zero Gold rRNA (Yeast) | Illumina | Cat#MRZY1324 |
| MicroPlex Library Preparation kit v2 | Diagenode | Cat#C05010014 |
| SPRIselect beads | Beckman-Coulter | Cat#B23319 |
| AMPure XP beads | Beckman-Coulter | Cat#A63882 |
| Deposited data | ||
| Raw and analyzed data 4sU RNA-seq | This paper | GEO: GSE175905 |
| Raw and analyzed data ATAC-seq | This paper | GEO: GSE175905 |
| Raw and analyzed data H3K9ac ChIP-seq | This paper | GEO: GSE175905 |
| Mass spectrometry proteomics Taf10 IP | This paper | PRIDE: PXD027026 |
| Mass spectrometry proteomics Mbip and Zzz3 IP | This paper | PRIDE: PXD027026 |
| Original western blot images | This paper | Mendeley Data: https://doi.org/10.17632/thjcm8zdpf.1 |
| Experimental models: Cell lines | ||
| Mouse: ES E14tg2a.4 cells (129P2 genetic background) | BayGenomics | N/A |
| Mouse: Supt7l−/− ES E14 cells | This study | N/A |
| Mouse: Supt7ltg ES E14 cells | This study | N/A |
| Mouse: Supt20h−/− ES E14 cells | This study | N/A |
| Mouse: Tada2b−/− ES E14 cells | This study | N/A |
| Mouse: Tada2b−/− ES E14 cells | This study | N/A |
| Mouse: Yeats2AID/AID ES E14 cells N-ter. | This study | N/A |
| Mouse: Tada3AID/AID ES E14 cells N-ter. | This study | N/A |
| Mouse: Zzz3AID/AID ES E14 cells N-ter. | This study | N/A |
| Mouse: Zzz3AID/AID ES E14 cells C-ter. | This study | N/A |
| D. melanogaster: Schneider S2 cells | ATCC | CRL-1963 |
| Experimental models: Organisms/strains | ||
| S. pombe: DHP43 h- | Elías-Villalobos et al., 2019 | N/A |
| S. cerevisiae: Strain background: FY406 | Hirschhorn et al., 1995 | N/A |
| Oligonucleotides | ||
| For sgRNA sequences, see Table S1 | This paper | N/A |
| For primer sequences, see Table S2 | This paper | N/A |
| Recombinant DNA | ||
| Plasmid: Supt7l CDS-HygromycinR | This paper | N/A |
| Plasmid: Cas9-eGFP-sgRNA against Supt7l for KO | This paper | N/A |
| Plasmid: Cas9-eGFP-sgRNA against Supt20h for KO | This paper | N/A |
| Plasmid: Cas9-mCherry-sgRNA against Tada2b for KO | This paper | N/A |
| Plasmid: Cas9-eGFP-sgRNA against Tada2a for KO | This paper | N/A |
| Plasmid: Cas9-eGFP-sgRNA against Yeats2 for KO | This paper | N/A |
| Plasmid: Cas9-eGFP-sgRNA against Zzz3 for KO | This paper | N/A |
| Plasmid: Tir1-IRES-BirA-NeomycinR | This paper | N/A |
| Plasmid: Cas9-mCherry-sgRNA against N-ter of Yeats2 for AID tagging | This paper | N/A |
| Homologous Recombination Plasmid for N-ter AID-tagging of Yeats2: eGFP-P2A-1xFlag-BioTag-AID |
This paper | N/A |
| Plasmid: Cas9-mCherry-sgRNA against N-ter of Tada3 for AID tagging | This paper | N/A |
| Homologous Recombination Plasmid for N-ter AID-tagging of Tada3: eGFP-P2A-1xFlag-BioTag-AID |
This paper | N/A |
| Plasmid: Cas9-mCherry-sgRNA against N-ter of Zzz3 for AID tagging | This paper | N/A |
| Homologous Recombination Plasmid for N-ter AID-tagging of Zzz3: eGFP-P2A-1xFlag-BioTag-AID | This paper | N/A |
| Plasmid: Cas9-mCherry-sgRNA against C-ter of Zzz3 for AID tagging | This paper | N/A |
| Homologous Recombination Plasmid for C-ter AID-tagging of Yeats2: AID-1xFlag-BioTag-P2A-eGFP | This paper | N/A |
| Software and algorithms | ||
| Fiji | Schindelin et al., 2012 | https://imagej.net/software/fiji/downloads |
| cutadapt | Martin, 2011 | https://cutadapt.readthedocs.io/en/v1.10/ |
| Bowtie2 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| STAR | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| htseq-count | Anders et al., 2015 | https://htseq.readthedocs.io/en/master/ |
| DESeq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Enrichr | Chen et al., 2013; Kuleshov et al., 2016; Xie et al., 2021 | https://maayanlab.doud/Enrichr/ |
| RTA | Illumina | https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/hiseq/hcs-hd-v3-4-0-install-notes-1000000028070-00.pdf |
| bcl2fastq | Illumina | https://emea.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html |
| Encode ATAC-seq pipeline | ENCODE | https://www.encodeproject.org/atac-seq/ |
| MACS2 | Zhang et al., 2008 | https://hbctraining.github.io/Intro-to-ChIPseq/lessons/05_peak_calling_macs.html |
| Homer v4.11.1 | Heinz et al., 2010 | http://homer.ucsd.edu/homer/ |
| Bedtools | Quinlan and Hall, 2010 | https://github.com/arq5x/bedtools2 |
| Enrichr | Kuleshov et al., 2016 | https://maayanlab.doud/Enrichr/ |
| WebGestalt GEne SeT Analysis Toolkit | Wang et al., 2013 | http://www.webgestalt.org/ |
| chromHMM datasets | Pintacuda et al., 2017 | https://github.com/guifengwei/ChromHMM_mESC_mm10 |
| ATACseqQC | Ou et al., 2018 | https://www.bioconductor.org/packages/release/bioc/html/ATACseqQC.html |
| Proteome Discoverer | ThermoFisher Scientific | https://www.thermofisher.com/fr/fr/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/multi-omics-data-analysis/proteome-discoverer-software.html |
| FlowJo™ | Ashland; Becton, Dickinson and Company | https://www.fiowjo.com/solutions/fiowjo/downloads |