KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-H3K9me3 | Abcam | Cat# ab8898; RRID: AB_306848 |
| anti-GFP (polyclonal ChIP-grade) | Abcam | Cat# ab290; RRID: AB_303395 |
| anti-GFP clones 7.1 and 13.1 | Roche | Cat# 11814460001; RRID: AB_390913 |
| anti-GFP (coupled to agarose beads, GFP-Trap®) | Chromotek | Cat# gta20; RRID: AB_2631357 |
| anti-c-Myc (9E10) | Santa Cruz | Cat# sc-40; RRID: AB_627268 |
| anti-c-Myc Agarose Affinity Gel antibody | Sigma-Aldrich | Cat# A7470; RRID: AB_10109522 |
| anti-FLAG® M2 Affinity Gel | Sigma-Aldrich | Cat# A2220; RRID: AB_10063035 |
| anti-FLAG® M2 antibody | Sigma-Aldrich | Cat# F3165; RRID: AB_259529 |
| anti-FLAG® antibody | Sigma-Aldrich | Cat# F7425; RRID: AB_439687 |
| anti-Swi6 (affinity purified) | (Nakayama et al., 2000) | N/A |
| IgG Sepharose 6 Fast Flow affinity resin | GE Healthcare | Cat# 17096901 |
| RFP booster_ATTO594 | Chromotek | Cat# rba594–100; RRID: AB_2631390 |
| Anti-Nuclear Pore Complex Proteins antibody (Mab414) | Abcam | Cat# ab24609; RRID: AB_448181 |
| Alexa Fluor® 647-conjugated goat anti-rabbit (F(ab’)2-Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody) |
Molecular Probes™, Thermo Fisher Scientific | Cat# A-21246; RRID: AB_2535814 |
| Alexa Fluor® 488-conjugated goat anti-rabbit (F(ab’)2-Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody) |
Molecular Probes™, Thermo Fisher Scientific | Cat# A-11017; RRID: AB_2534084 |
| Mouse IgG HRP Linked Whole Ab | GE Healthcare | Cat# NA931; RRID: AB_772210 |
| Rabbit IgG HRP Linked Whole Ab | GE Healthcare | Cat# NA934; RRID: AB_772206 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| iTaq™ Universal SYBR® Green Supermix | BioRad | Cat# 1725122 |
| Lectin from Glycine max (soybean) | Sigma-Aldrich | Cat# L1395 |
| 16% Paraformaldehyde aqueous | Electron Microscopy Sciences | Cat# 15710 |
| 8% glutaraldehyde | Electron Microscopy Sciences | Cat# 16019 |
| Zymolyase 100T | MP Biomedicals | Cat# SKU 08320932 |
| VECTASHIELD® Antifade Mounting Medium | Vector Laboratories | Cat# H-1000 |
| Paraformaldehyde | Sigma-Aldrich | Cat# P6148 |
| ProLong™ Gold antifade mountant with DAPI | Molecular Probes™, Thermo Fisher Scientific | Cat# P36931 |
| TetraSpeck™ Microspheres, 0.1 µm, fluorescent blue/green/orange/dark red | Molecular Probes™, Thermo Fisher Scientific | Cat# T7279 |
| Trichloroacetic acid solution | Sigma-Aldrich | Cat# T0699 |
| 3-[(3-Cholamidopropyl)dimethylammonio]-1-propanesulfonate hydrate, CHAPS | Sigma-Aldrich | Cat# 226947 |
| cOmplete™, Mini Protease Inhibitor Cocktail | Roche, Sigma-Aldrich | Cat# 11836153001 |
| Phenylmethanesulfonyl fluoride (PMSF) | Sigma-Aldrich | Cat# P7626 |
| 4–12% Bis-Tris PAGE | Thermo Fisher Scientific | Cat# NP0321BOX |
| SimplyBlue™ SafeStain | Thermo Fisher Scientific | Cat# LC6060 |
| anti-c-Myc Peptide | Sigma-Aldrich | Cat# M2435 |
| AcTEV™ Protease | Thermo Fisher Scientific | Cat# 12575015 |
| Dimethyl adipimidate (DMA) | Sigma-Aldrich | Cat# 285625 |
| Protein A Sepharose® 4B Conjugate | Thermo Fisher Scientific | Cat# 101041 |
| Recombinant Protein G Agarose | Thermo Fisher Scientific | Cat# 15920010 |
| PureLink RNase A | Thermo Fisher Scientific | Cat# 12091039 |
| Proteinase K solution | Thermo Fisher Scientific | Cat# AM2548 |
| Amminoallyl-dUTP | Thermo Fisher Scientific | Cat# R1101 |
| Cyanine5 NHS ester | Lumiprobe | Cat# 23020 |
| Cyanine3 NHS ester | Lumiprobe | Cat# 21020 |
| HybondTM-N+ | Fisher Scientific | Cat# 45–000850 |
| α-P32-UTP | Perkin Elmer | Cat# BLU007H250uc |
| UltraHyb-oligo hybridization buffer | Ambion, Thermo Fisher Scientific | Cat# AM8663 |
| Cy3-dCTP | Amersham, GE Healthcare | Cat# PA53021 |
| AluI, DdeI, RsaI, HaeIII, NotI-HF | New England Bio Labs | Cat# R0137, R0175, R0167, R0108, R3189 |
| Hydroxyurea | Sigma-Aldrich | Cat# H8627 |
| SYTOX™ Green Nucleic Acid Stain | Thermo Fisher Scientific | Cat# S7020 |
| Critical Commercial Assays | ||
| In-Fusion® HD Cloning Plus Kit | Takara Bio USA, Inc. | Cat# 638909 |
| MasterPure™ Yeast RNA Purification Kit | Lucigen | Cat# MPY03100 |
| SuperScript-III Reverse Transcriptase | Invitrogen, Thermo Fisher Scientific | Cat# 18080044 |
| QIAquick PCR Purification kit | Qiagen | Cat# 28106 |
| NEBNext Ultra II DNA library prep kit for Illumina | New England Bio Labs | Cat# E7645S |
| MAXIscript T7 Transcription kit | Ambion, Thermo Fisher Scientific | Cat# AM1312 |
| mirVana miRNA isolation kit | Ambion, Thermo Fisher Scientific | Cat# AM1560 |
| Random Primer DNA Labeling Kit Ver. 2 | Takara Bio USA, Inc. | Cat# 6045 |
| Deposited Data | ||
| ChIP-chip analysis of H3K9me3 and RIXC subunit enrichments, and histone turnover assay | This study | GEO: GSE132865 |
| ChIP-seq analysis of Rix1 distribution | This study | GEO: GSE132865 |
| Experimental Models: Organisms/Strains | ||
| S. pombe strains, see Table S2 | Grewal lab and this study | N/A |
| Oligonucleotides | ||
| Oligo(dT)12–18 Primer | Thermo Fisher Scientific | Cat# 18418012 |
| Random Hexamer Primer | Thermo Fisher Scientific | Cat# SO142 |
| RT-qPCR, ChIP-qPCR, Northern blot probe, DNA FISH probe, see Table S3 | This study | N/A |
| Software and Algorithms | ||
| Trimmomatic | (Bolger et al., 2014) | http://www.usadellab.org/cms/?page=trimmomatic |
| BWA-MEM | (Li and Durbin, 2010) | http://bio-bwa.sourceforge.net/bwa.shtml |
| SAMtools mpileup/ BCFtools | (Li, 2011) | https://samtools.github.io/bcftools/bcftools.html |
| SnpEff | (Cingolani et al., 2012) | http://snpeff.sourceforge.net/SnpEff_manual.html |
| Picard Tools | Broad Institute | http://broadinstitute.github.io/picard |
| Bedtools | Quinlan laboratory, The University of Utah | https://bedtools.readthedocs.io/en/latest/index.html |
| SoftWoRx | Applied Precision, GE Healthcare | http://incelldownload.gehealthcare.com/bin/download_data/SoftWoRx/6.5.2/SoftWoRx.htm |
| Fiji | ImageJ | https://imagej.net/Using_Fiji |
| GraphPad Prism 8 software | GraphPad Software Inc. | https://www.graphpad.com/data-analysis-resource-center/#guides |
| Proteome Discoverer Software Version 2.2 | Thermo Fisher Scientific | https://assets.thermofisher.com/TFS-Assets/CMD/manuals/Man-XCALI-97808-Proteome-Discoverer-User-ManXCALI97808-EN.pdf |
| FlowJo software | FlowJo LLC | https://www.flowjo.com/solutions/flowjo/downloads/tutorials |