KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
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| ||
| Antibodies | ||
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| Anti-HHV-8 LNA-1 Antibody, clone LN53 | Sigma-Aldrich | Cat# MABE1109 |
| CHD4 (D4B7) Rabbit mAb | Cell Signaling Technology | Cat# 12011S; RRID: AB_2734702 |
| ADNP Polyclonal Antibody | Thermo Fisher | Cat# PA5-52286; RRID: AB_2637725 |
| Monoclonal ANTI-FLAG® M2 antibody produced in mouse | Sigma-Aldrich | Cat# F1804; RRID: AB_262044 |
| Acetyl-Histone H3 (Lys27) (D5E4) XP® Rabbit mAb | Cell Signaling Technology | Cat# 8173; RRID: AB_10949503 |
| Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb | Cell Signaling Technology | Cat# 9733; RRID: AB_2616029 |
| Mono-Methyl-Histone H3 (Lys4) (D1A9) XP® Rabbit mAb | Cell Signaling Technology | Cat# 5326; RRID: AB_10695148 |
| Anti-RNA polymerase II Antibody, clone CTD4H8 | Sigma-Aldrich | Cat# 05-623; RRID:AB_309852 |
| Anti-mouse IgG, HRP-linked Antibody | Cell Signaling Technology | Cat# 7076; RRID: AB_330924 |
| Anti-rabbit IgG, HRP-linked Antibody | Cell Signaling Technology | Cat# 7074; RRID: AB_2099233 |
| Anti-β-Actin antibody, Mouse monoclonal | Sigma-Aldrich | Cat# A1978; RRID: AB_476692 |
| normal mouse IgG | Santa Cruz Biotechnology | Cat# sc-2025; RRID: AB_737182 |
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| Bacterial and virus strains | ||
|
| ||
| KSHV virions from iSLK.219 | In this study | N/A |
| KSHV virions from iSLK LANA-mTID | In this study | N/A |
| KSHV virions from iSLK.BAC16 | In this study | N/A |
|
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| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| Lipofectamine RNAiMAX | Invitrogen | Cat# 13778150 |
| Lipofectamine 2000 | Invitrogen | Cat# 11668019 |
| Protease inhibitor cocktail | Sigma-Aldrich | Cat# 11697498001 |
| D-Biotin | Invitrogen | Cat# B1595 |
| Pierce™ Streptavidin Magnetic Beads | Thermo Scientific | Cat# 88816 |
| Streptavidin, horseradish peroxidase conjugate | Invitrogen | Cat# S911 |
| Hygromycin B | Enzo | Cat# ALX-380-306-G001 |
| Puromycin | InvivoGen | Cat# ant-pr-1 |
| G418 | InvivoGen | Cat# ant-gn-1 |
| Blasticidin | InvivoGen | Cat# ant-bl-05 |
| DMEM, high glucose | Gibco | Cat# 11965092 |
| RPMI 1640 Medium | Gibco | Cat# 61870036 |
| FBS | Gibco | Cat# 26140-079 |
| Opti-MEM™ I Reduced Serum Medium | Gibco | Cat# 31985062 |
| Penicillin-Streptomycin-Glutamine (100X) | Gibco | Cat# 10378016 |
| Trypsin-EDTA (0.5%) | Gibco | Cat# 15400054 |
| CHD4 protein | In this study | N/A |
| LANA protein | In this study | N/A |
| ADNP protein | In this study | N/A |
| GST protein | In this study | N/A |
| GST LANA 4–150, 50–200, 100–250, 150–330, 870–1020, 870–1070, 1020–1162 | In this study | N/A |
| Luciferase protein | In this study | N/A |
| Spermidine | Sigma-Aldrich | Cat# S2626 |
| BioMag®Plus Concanavalin A | Polysciences | Cat# 86057-10 |
| Digitonin | Spectrum | Cat# DI120 |
| pAG-MNase | In this study | N/A |
| RNAase A | Macherey-Nagel | Cat# 740505 |
| AMPure XP paramagnetic beads | Beckman | Cat# A63880 |
|
| ||
| Critical commercial assays | ||
|
| ||
| Arima-HiC kit | Arima Genomics | N/A |
| HiScribe™ T7 High Yield RNA Synthesis Kit | NEB | Cat# E2040S |
| NEBuilder® HiFi DNA Assembly Master Mix | NEB | Cat# E2621L |
|
| ||
| Deposited data | ||
|
| ||
| CHi-C | In this study | GEO: GSE163694 |
| CUT&RUN | In this study | GEO: GSE163098 |
|
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| Experimental models: Cell lines | ||
|
| ||
| Human: iSLK.219 | Myoung and Ganem, 2011 | N/A |
| Human: TREx BCBL1 | Nakamura et al., 2003 | N/A |
| Human: 293FT | Invitrogen | Cat# R70007 |
| Human: BC1 | ATCC | CRL-2230 |
| Human: BC3 | ATCC | CRL-2277 |
| Human: BCBL1 | Renne et al., 1998 | N/A |
| Human: iSLK LANA-mTID | In this paper | N/A |
| Human: iSLK | Myoung and Ganem, 2011 | N/A |
| Human: iSLK mTID-57 PAN Wt | In this paper | N/A |
| Human: iSLK mTID-57 PAN Mt | In this paper | N/A |
|
| ||
| Oligonucleotides | ||
|
| ||
| Primer for qPCR | In this paper | Table S3 |
| ORF57 TurboID FW Recombination: GCTGCCAGGTTCCCAAAATAGCCC GCGGCATACGGCTCACTTCCCCCC ACATTCCCCCCCGTGCACAATATAA GAACCAAAGGACATGGATTATAAGG ATGATGACAAGGGGGAC |
In this paper | N/A |
| ORF57 TurboID RV Recombination: AGAAATGGGAAAAGTCTGTTGTAG ACGAGGACTTACCCTCTAGGATGC CCTTCATAATGTCCATGTCTATCAT TGCTTGTACGTCCGCTCGGCTAAA CTCCTTCTCTGCACTTC |
In this paper | N/A |
| LANA Turbo ID FW Recombination: CCTTGTGGTCACTACGGGTATTGC ATAATGTGAATATACTGCCACCGC CTCCATAATTTTACTTTGGTTGTCA GACCAGATTTCCCGAGGATGGATT ATAAGGATGATGACAAGGGGGAC |
In this paper | N/A |
| LANA TurboID RV Recombination: | ||
| CTGTTTCGTTTCCTACAACTTCCTC TCGTTAAGGGCGCGCCGGTGCTC CGTCCCGACCTCAGGCGCATTCC CGGGGGCGCGTCCGCTCGGCTA AACTCCTTCTCTGCACTTCTGAGA |
In this paper | N/A |
| siRNA targeting sequence | In this paper | Table S4 |
| In vitro PAN RNA interaction assay | In this paper | Table S5 |
| Custom-designed KSHV genomic capture probe library | IDT | N/A |
|
| ||
| Recombinant DNA | ||
|
| ||
| CHD4 (NM_001273) Human Tagged ORF Clone | Origene | Cat# RC224232L1 |
| Chd4 (NM_145979) Mouse Tagged ORF Clone | Origene | Cat# MR212098 |
|
| ||
| Software and algorithms | ||
|
| ||
| GraphPad Prism 8.0.1 | GraphPad | https://www.graphpad.com; RRID: SCR_002798 |
| FlowJo | TreeStar | https://www.flowjo.com; RRID: SCR_008520 |
| Integrative Genomics Browser (IGV) 2.8.2 | Broad Institute | http://www.broadinstitute.org/igv/; RRID: SCR_011793 |
| Scaffold proteome software 4.11.0 | Proteome software | http://www.proteomesoftware.com/products/scaffold/; RRID: SCR_014345 |
| Excel | Microsoft | https://products.office.com/ |
| HiC-pro 2.11.1 pipeline | Servant et al., 2015 | N/A |
| Intervene v0.6.4 | Khan and Mathelier, 2017 | N/A |
| HiCUP (v0.7.4) pipeline | Wingett et al., 2015 | N/A |
| Bowtie2 v2.3.5.1 | Langmead and Salzberg, 2012 | N/A |
| HISAT2 v2.1.0 | Kim et al., 2019 | N/A |
| MACS2 | Zhang et al., 2008 | N/A |
| NGS plot v2.63 | Shen et al., 2014 | N/A |
| Seura” R package | Stuart et al., 2019 | N/A |