KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit anti-SON | Custom made against hSON peptide (947–964; Cys-DPYRLGHDPYRLTPDPYR) | Pacific Immunology Corp. |
| Anti-Lamin B1 antibody | Abcam | ab16048 |
| Anti-MKI67IP antibody | Atlas Antibodies | HPA035735 |
| GFP Monoclonal Antibody (3E6) | ThermoFisher Scientific | A-11120 |
| Anti-RNA Pol II Ser5P monoclonal antibody, clone CTD4H8 | Millipore-Sigma | 05-623 |
| Acetyl-Histone H3 (Lys27) (D5E4) Rabbit Monoclonal Antibody | Cell Signaling Technology | 8173S |
| ZNF384 Polyclonal Antibody | ThermoFisher Scientific | PA5-52044 |
| Normal Goat IgG (for ChIP assay) | Cell Signaling Technology | 2729S |
| Normal goat serum | Millipore-Sigma | G9023 |
| Alexa Fluor® 488 AffiniPure Goat Anti-Mouse IgG | Jackson Immunoresearch Inc. | 115-545-146 |
| Alexa Fluor® 647 AffiniPure Goat Anti-Mouse IgG | Jackson Immunoresearch Inc. | 115-605-174 |
| Alexa Fluor® 594 AffiniPure Goat Anti-Rabbit IgG | Jackson Immunoresearch Inc. | 111-585-003 |
| Fluorescein (FITC) AffiniPure® Goat Anti-Rabbit IgG (H+L) | Jackson Immunoresearch Inc. | 111-095-144 |
| Rhodamine Red-X (RRX) AffiniPure™ Goat Anti-Rabbit IgG | Jackson Immunoresearch Inc. | 111-296-003 |
| Alexa Fluor® 647 AffiniPure® Goat Anti-Rabbit IgG (H+L) | Jackson Immunoresearch Inc. | 111-605-144 |
| Streptavidin, Alexa Fluor™ 594 Conjugate | ThermoFisher Scientific | S11227 |
| Alexa Fluor® 647 Streptavidin | Jackson Immunoresearch Inc. | 016-600-084 |
| Alexa Fluor® 594 AffiniPure® Goat Anti-Mouse IgG (H+L) | Jackson Immunoresearch Inc. | 115-585-146 |
| Alexa Fluor® 647 IgG Fraction Monoclonal Mouse Anti-Digoxin | Jackson Immunoresearch Inc. | 200-602-156 |
| Chemicals, peptides, and recombinant proteins | ||
| Janelia Fluor® 646 HaloTag® Ligand | Promega | GA1120 |
| Triptolide | Millipore-Sigma | T3652 |
| DRB | Millipore-Sigma | D1916 |
| Nocodazole | Millipore-Sigma | M1404 |
| DMSO | Millipore-Sigma | D2650-5x10mL |
| Fibronectin | Millipore-Sigma | F1141 |
| Bovine Serum Albumin | Millipore-Sigma | A7906 |
| 5-Ethynyl uridine (EU) | Jena Bioscience | CLK-N002-10 |
| Digoxigenin-11-dUTP, alkali-stable | Millipore-Sigma | 11093088910 |
| Biotin-14-ATP | ThermoFisher Scientific | 19524016 |
| Glass coverslips #1.5, 12mm diameter | Fisher Scientific | 12-545-81 |
| Mouse Cot-1 DNA | ThermoFisher Scientific | 18440016 |
| Human Cot-1 DNA | ThermoFisher Scientific | 15279011 |
| G-418 Sulfate | Fisher Bioreagents | BP673-1 |
| Zeocin Selection Reagent | ThermoFisher Scientific | R25001 |
| Chloramphenicol | Millipore-Sigma | 220551-25GM |
| Blasticidin S HCl | ThermoFisher Scientific | R21001 |
| Hygromycin B (50 mg/mL) | ThermoFisher Scientific | 10687010 |
| Puromycin | Gibco | A11138-03 |
| Polybrene | Millipore-Sigma | TR-1003-G |
| Lipofectamine 2000 | ThermoFisher Scientific | 11668019 |
| Formamide, Deionized | Millipore-Sigma | S4117 |
| 5-Bromo-2′-deoxyuridine (BrdU) | Millipore-Sigma | B5002-250MG |
| 5-Bromo-2′-deoxycytidine (BrdC) | ThermoFisher Scientific | AAJ6545603 |
| bisBenzimide H 33258 (Hoechst 33258) | Millipore-Sigma | B2883-25MG |
| Exonuclease III (E.Coli) | New England Biolabs | M0206S |
| Roche cOmplete Mini EDTA-free tablets | Millipore-Sigma | 11836170001 |
| ChIP-Grade Protein G Magnetic Beads | Cell Signaling Technology | 9006S |
| RIPA Buffer (10X) | Cell Signaling Technology | 9806S |
| ChIP Wash Buffer | Santa Cruz Biotechnology | sc-45002 |
| Tamoxifen | Millipore-Sigma | T5648 |
| DAPI | Millipore-Sigma | D9542 |
| Paraformaldehyde | Millipore-Sigma | P6148-500G |
| Bacterial strains | ||
| DH5a Escherichia coli strain | New England Biolabs | C2984I |
| SW102 | Published earlier.33 | E. Coli recombineering strain |
| Experimental models: Cell lines | ||
| HCT116 (human colon carcinoma) | 4D Nucleome Consortium | ATCC-CCL-247 |
| hTERT RPE1 (human retinal pigment epithelial) | 4D Nucleome Consortium | ATCC CRL4000 |
| NIH 3T3 (mouse fibroblast) | ATCC | CRL-1658 |
| HEK293T cells | ATCC | CRL-3216 |
| Oligonucleotides | ||
| Oligonucleotides | Integrated DNA Technologies (IDT) | See Table S1 |
| Recombinant DNA | ||
| pMini-HB-attB-Neo-Puro-HSVtk-PB (hereafter Ctrl V1.0 vector) | See Table S1 | This study |
| pMini-HB-attB-Neo (hereafter Ctrl V2.0 vector) | See Table S1 | This study |
| pX330A-1x3 | Addgene | Plasmid # 58767 |
| FRT-PGK-FRT-attP-Puro-DTA plasmid | Gifted by David Gilbert, SDBRI | N/A |
| attB-Neo-SacB | Gifted by David Gilbert, SDBRI | N/A |
| pJoyC030 | Gifted by Bas van Steensel, NKI | N/A |
| mPB-L3-ERT2-tatRRR-mCherry | Gifted by Bas van Steensel, NKI | N/A |
| CTD-318A47 (human RTEL1 BAC) | ThermoFisher Scientific | Catalog #: 96012, Clone Id: 3184A7 |
| CTD-2269C15 (human COL1A2 BAC) | ThermoFisher Scientific | Catalog #: 96012, Clone Id: 2269C15 |
| RP11-765O14 (human ACTG1 BAC) | ThermoFisher Scientific | Catalog #: RPCI11.C, Clone Id: 765O14 |
| RP11-369N23 (human GAPDH BAC) | ThermoFisher Scientific | Catalog #: RPCI11.C, Clone Id: 369N23 |
| RP11-267M22 (human COL1A1 BAC) | ThermoFisher Scientific | Catalog #: RPCI11.C, Clone Id: 267M22 |
| RP11-92G8 (human HSPA1 BAC) | ThermoFisher Scientific | Catalog #: RPCI11.C, Clone Id: 92G8 |
| RP11-351B23 (human TPTE BAC) | ThermoFisher Scientific | Catalog #: RPCI11.C, Clone Id: 351B23 |
| RP11-715G8 (human OR51 BAC) | ThermoFisher Scientific | Catalog #: RPCI11.C, Clone Id: 715G8 |
| RP11-1136P2 (human RNPS1 BAC) | ThermoFisher Scientific | Catalog #: RPCI11.C, Clone Id: 1136P2 |
| RP11-634L10 (human ARHGDIA BAC) | ThermoFisher Scientific | Catalog #: RPCI11.C, Clone Id: 634L10 |
| RP23-99P16 (mouse BAC) | BACPAC Genomics Inc | Clone Id: RP23-99P16 |
| CITB-057L22 (mouse Dhfr/Msh3 BAC) | Published earlier.32 | Gifted by Edith Heard (Curie Institute, Paris, France) |
| Critical Commercial Assays | ||
| End-It DNA End-Repair Kit | Epicentre Biotech | ER0720 |
| TruSeq ChIP Library Preparation Kit – Set A | Illumina | IP-202-1012 |
| NEB® PCR Cloning Kit | New England Biolabs | E1203S |
| QIAGEN Large Construct Kit | QIAGEN | 12462 |
| Dneasy Blood & Tissue kit | QIAGEN | 69504 |
| QIAGEN Plasmid Midi Kit | QIAGEN | 12143 |
| QIAprep Spin Miniprep Kit | QIAGEN | 27106 |
| Deposited data | ||
| RPE1 SON TSA-Seq (G1 phase cells) | This study | Accession No. 4DNESKYNUNSG, 4DNESRI54D3Q, 4DNESGE6ZI4N, and 4DNESJ4OXHI8 |
| RPE1 SON TSA-Seq (log phase cells) | This study | Accession No. 4DNESNXH2OHP, 4DNESF79UZDD, 4DNESANW8A1W, and 4DNES3LO4836 |
| HCT116 SON TSA-Seq (used in Figure S1) | This study | Accession No. 4DNESQQ92325 and 4DNESUTJFN2R |
| NIH 3T3 SON TSA-Seq | This study | Accession No. 4DNESPRABC27 |
| NIH 3T3 LB1 TSA-Seq | This study | Accession No. 4DNES8Y37MM4 |
| HCT116 SON TSA-Seq | Published earlier.20 | Accession no. 4DNFI9GKAT7E |
| HFF SON TSA-Seq | Published earlier.20 | Accession no. 4DNFIW688BVB |
| HCT116 LB1 TSA-Seq | Published earlier.73 | Accession no. 4DNESTE8NJOE |
| HCT116 MKI67IP TSA-Seq | Published earlier.73 | Accession no. 4DNESAHA7E69 |
| H3K27ac ChIP-Seq on mouse embryonic fibroblast (MEF) | Published earlier.74 | Accession no. ENCSR000CDI |
| NIH 3T3 RNA-Seq | Published earlier.42 | Accession no. GSM5388182 |
| Image source data for Figure images | This study | doi: 10.17632/rjwkxm566p.1 |
| Softwares and algorithms | ||
| SnapGene Viewer | SnapGene | https://www.snapgene.com/ |
| ApE plasmid editor | M. Wayne Davis, University of Utah | https://jorgensen.biology.utah.edu/wayned/ape/ |
| Fiji (imageJ) | ImageJ | https://fiji.sc/ |
| Genomic loci to compartment distance ImageJ plugin | Github | https://github.com/omidalam/compartment_dist |
| Python | https://www.python.org/ | |
| R | https://www.r-project.org/ | |