KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| ZNF207 | Invitrogen | Cat#703747; RRID: AB_2815340 |
| ZNF207 | ThermoFisher Scientific | Cat#PA530641; RRID: AB_2548115 |
| FLAG M2 | Sigma | Cat#F3165; RRID: AB_259529 |
| GAPDH | Proteintech | Cat#10494–1-AP; RRID: AB_2263076 |
| SF3B1 | Proteintech | Cat#27684–1-AP; RRID: AB_2880946 |
| PRPF6 | Proteintech | Cat#23929–1-AP; RRID: AB_2879365 |
| SNRNP200 | Proteintech | Cat#23875–1-AP; RRID: AB_2879346 |
| RBM25 | Proteintech | Cat#25297–1-AP; RRID: AB_2880014 |
| SNRNP70 | Abcam | Cat#ab83306; RRID: AB_10673827 |
| SNRPA | Proteintech | Cat#10212–1-AP; RRID: AB_2239723 |
| SNRPC | Proteintech | Cat# 22428–1-AP; RRID: AB_2918077 |
| SNRPF | Proteintech | Cat#14977–1-AP; RRID: AB_2302166 |
| BUB3 | ThermoFisher Scientific | Cat#BDB611730; RRID: AB_2243620 |
| HA tag | Sigma-Aldrich | Cat#H3663; RRID: AB_262051 |
| Beta-actin | Proteintech | Cat#20536–1-AP; RRID: AB_10700003 |
| Lamin A/C | Santa Cruz Biotechnology | Cat#sc376248; RRID: AB_10991536 |
| LAP2 alpha | Abcam | Cat#ab5162; RRID: AB_304757 |
| Lamin B1 | Abcam | Cat#ab16048; RRID: AB_443298 |
| Histone H3 (tri methyl K27) | Abcam | Cat#ab192985; RRID: AB_2650559 |
| Acetyl-Histone H4 (acetyl K16) | Abcam | Cat#ab109463; RRID: AB_10858987 |
| Anti-rabbit IgG, HRP-linked Antibody | Cell Signaling Technology | Cat#7074; RRID: AB_2099233 |
| Anti-mouse IgG, HRP-linked Antibody | Cell Signaling Technology | Cat#7076; RRID: AB_330924 |
| Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 594 | Invitrogen | Cat#A11012; RRID: AB_2534079 |
| Bacterial and virus strains | ||
| NEB Stable competent E. coli cells | New England Biolabs | Cat#C3040H |
| Endura electrocompetent cells | LGC Biosearch Technologies | Cat#60242–2 |
| One Shot™ BL21(DE3) Chemically Competent E. coli | ThermoFisher Scientific | Cat#C600003 |
| Chemicals, peptides, and recombinant proteins | ||
| TRIzol | Sigma-Aldrich | Cat#T3934 |
| Puromycin | ThermoFisher Scientific | Cat#A1113803 |
| G418 Sulfate | Gibco | Cat#10131027 |
| Blasticidin S | Gibco | Cat#A1113903 |
| Hygromycin | ThermoFisher Scientific | Cat#10687010 |
| Doxycycline | Sigma-Aldrich | Cat#D9891 |
| Polybrene | Sigma-Aldrich | Cat#H9268 |
| DTT (dithiothreitol) | ThermoFisher Scientific | Cat#R0861 |
| D-Biotin | ThermoFisher Scientific | Cat#B20656 |
| IGEPAL® CA-630 | Sigma-Aldrich | Cat#I3021 |
| DAPI | Biotium | Cat#40043 |
| ATP | ThermoFisher Scientific | Cat#R0441 |
| Creatine phosphate | Sigma-Aldrich | Cat#10621714001 |
| Polyvinyl alcohol (PVA) | ThermoFisher Scientific | Cat#041241.22 |
| ZNF207 full-length | This study | N/A |
| ZNF207 K42E | This study | N/A |
| ZNF207 1–122 (ZnF+Hel) | This study | N/A |
| ZNF207 1–122 K42E (ZnF+Hel_K42E) | This study | N/A |
| U1–70K (SNRNP70) 1–216 | This study | N/A |
| U1-A (SNRPA) | This study | N/A |
| U1-C (SNRPC) | This study | N/A |
| Critical commercial assays | ||
| RNeasy Plus Mini Kit | Qiagen | Cat#74136 |
| DNA Gel Loading Dye (6X) | ThermoFisher Scientific | Cat#R0611 |
| NEBNext Ultra II Q5 Master Mix | New England Biolabs | Cat#M0544X |
| Q5® Site-Directed Mutagenesis Kit (Without Competent Cells) | New England Biolabs | Cat#E0552S |
| QIAquick PCR Purification Kit | Qiagen | Cat#28104 |
| GeneJET PCR purification column | ThermoFisher Scientific | Cat#K0701 |
| GeneJET Gel Extraction Kit | ThermoFisher Scientific | Cat#K0691 |
| SYBR Safe | ThermoFisher Scientific | Cat#S33102 |
| Chemiluminescent Nucleic Acid Detection Module Kit | ThermoFisher Scientific | Cat#89880 |
| Streptavidin-Horseradish Peroxidase (HRP) Conjugate | ThermoFisher Scientific | Cat#SA10001 |
| EasyPep™ MS Sample Prep Kits | ThermoFisher Scientific | Cat#A57864 |
| KAPA HiFi HotStart DNA polymerase | Roche | Cat# KK2601 |
| D1000 ScreenTape | Agilent | Cat#5067–5582; Cat#5067–5583 |
| High Sensitivity D1000 ScreenTape | Agilent | Cat#5067–5584 |
| High Sensitivity D1000 Reagents | Agilent | Cat#5067–5585 |
| RNA ScreenTape | Agilent | Cat#5067–5576 |
| RNA ScreenTape Sample Buffer | Agilent | Cat#5067–5577 |
| Qubit dsDNA HS assay | ThermoFisher Scientific | Cat#Q32851 |
| PhiX | Illumina | Cat#FC-110–3001 |
| NovaSeq™ X Series 1.5B Reagent Kit (300 Cyc) | Illumina | Cat# 20104704 |
| NovaSeq™ X Series 1.5B Reagent Kit (300 Cyc) | Illumina | Cat# 20104705 |
| Illumina Stranded mRNA Prep kit | Illumina | Cat#15031047 |
| In-Fusion Snap Assembly Master Mix | Takara Bio | Cat#638948 |
| NEBuilder HiFi DNA Assembly Master Mix | New England Biolabs | Cat#E2621L |
| X-tremeGENE 9 DNA Transfection Reagent | Sigma-Aldrich | Cat#6365809001 |
| QIAGEN OneStep RT-PCR Kit | Qiagen | Cat#210215 |
| SensiFAST™ SYBR® No-ROX Kit | Bioline | Cat#BIO-98050 |
| Maxima H Minus First Strand cDNA Synthesis Kit | ThermoFisher Scientific | Cat#K1651 |
| SensiFAST™ SYBR® No-ROX One-Step Kit | Bioline | Cat#BIO-72005 |
| Maxi-prep plasmid purification kit | Invitrogen | Cat#K210016 |
| EndoFree Plasmid Maxi Kit | Qiagen | Cat#12362 |
| BP clonase II | ThermoFisher Scientific | Cat#11789020 |
| LR clonase II | ThermoFisher Scientific | Cat#11791020 |
| BveI | ThermoFisher Scientific | Cat#FD1744 |
| Eco47III | ThermoFisher Scientific | Cat#FD0324 |
| Eco32I | ThermoFisher Scientific | Cat#FD0304 |
| KpnI | New England Biolabs | Cat#R3142L |
| NdeI | New England Biolabs | Cat#R0111L |
| BamHI | New England Biolabs | Cat#R0136L |
| NcoI | New England Biolabs | Cat#R0193L |
| FastAP | ThermoFisher Scientific | Cat#EF0651 |
| RNase Inhibitor, Murine | New England Biolabs | Cat#M0314L |
| T4 RNA Ligase 1 (ssRNA Ligase) | New England Biolabs | Cat#M0204L |
| T4 DNA ligase | New England Biolabs | Cat#M0202 |
| Amylose Resin | New England Biolabs | Cat#E0821S |
| HiScribe® T7 High Yield RNA Synthesis Kit | New England Biolabs | Cat#E2040S |
| Lipofectamine RNAiMax | ThermoFisher Scientific | Cat#13778150 |
| Lipofectamine™ 2000 Transfection Reagent | ThermoFisher Scientific | Cat#11668027 |
| Streptavidin Sepharose Beads | ThermoFisher Scientific | Cat#20353 |
| Dynabeads protein G | ThermoFisher Scientific | Cat#10004D |
| Dynabeads™ Oligo(dT)25 | ThermoFisher Scientific | Cat#61002 |
| Proteinase-K | ThermoFisher Scientific | Cat#EO0492 |
| mMESSAGE mMACHINE™ T7 mRNA Kit with CleanCap™ Reagent AG | Invitrogen | Cat#A57620 |
| RNaseA | Invitrogen | Cat#12091021 |
| HELA NUCLEAR EXTRACT for pre-mRNA splicing | Protein One | Cat#P0002–02 |
| Bicinchoninic acid (BCA) assay | Pierce | Cat#23225 |
| Bradford reagent | BioRad | Cat#5000006 |
| NuPAGE LDS Sample Buffer (4x) | ThermoFisher Scientific | Cat# NP0007 |
| cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail | Roche | Cat#11836170001 |
| cOmplete™ Protease Inhibitor Cocktail | Roche | Cat#11836145001 |
| Protease Inhibitor Cocktail III | Sigma-Aldrich | Cat#539134–1ML |
| 4–12% Bis-Tris gels | Life Technologies | Cat#NP0323BOX |
| Immobilon-P PVDF membrane | Sigma-Aldrich | Cat#IPVH00010 |
| Benzonase® Nuclease | Sigma-Aldrich | Cat#E1014 |
| SuperSignal West Pico PLUS chemiluminescence reagent | ThermoFisher Scientific | Cat#34580 |
| SuperSignal™ Western Blot Substrate Bundle, Femto + trial-size Atto | ThermoFisher Scientific | Cat#A45916 |
| DMEM with high glucose and pyruvate | Gibco | Cat#11995073 |
| heat-inactivated fetal bovine serum (HI-FBS) | Gibco | Cat#16140071 |
| penicillin-streptomycin | Gibco | Cat#15140122 |
| trypsin-EDTA | Gibco | Cat#25200056 |
| Opti-MEM | Gibco | Cat#31985062 |
| MEM, no glutamine | Gibco | Cat#11090081 |
| L-Glutamine (200 mM) | Gibco | Cat#25030081 |
| MEM Non-Essential Amino Acids Solution (100X) | Gibco | Cat#11140050 |
| Sequencing Grade Modified Trypsin | Promega | Cat#V5111 |
| PhenoPlate™ 384-well microplates | Revvity Health Sciences | Cat#6057300 |
| Deposited data | ||
| CRASP-Seq data | This study | GEO: GSE284628 |
| ZNF207 RNA-Seq | This study | GEO: GSE284629, GSE284630 |
| ZNF207 eCLIP-Seq data | This study | GEO: GSE284631 |
| ZNF207 miniTurboID data | This study | proteomXchange: MSV000096693 |
| Unprocessed Imaging data | This study | Mendeley Data: 10.17632/xvzfdm8kky.1 |
| Experimental models: Cell lines | ||
| HAP1 Cas9/Cas12a | This study | N/A |
| HAP1 highly efficient adenine base editor (ABE8e) | Xiao et al.11 | N/A |
| HAP1 cytosine base editor (evoCDA1) | Xiao et al.11 | N/A |
| RPE1 hTERT TP53 −/− Cas9/Cas12a | This study | N/A |
| HEK293T | ATCC | Cat#ACS-4500 |
| HEK293 Flp-In T-REx cells | Invitrogen | Cat#R78007 |
| HepG2 Cas9/Cas12a | This study | N/A |
| hTERT-immortalized fibroblasts | Fernandez et al.77 | N/A |
| hTERT-immortalized fibroblasts HGPS | Fernandez et al.77 | N/A |
| Oligonucleotides | ||
| See Table S2 | This study | N/A |
| Recombinant DNA | ||
| See Table S2 and STAR Methods | This study | N/A |
| Plasmids | This study | https://www.addgene.org/depositing/85289/ |
| Libraries | This study | https://www.addgene.org/pooled-library/gonatopoulos-pournatzis-human-crispr-crasp-seq/ |
| Software and algorithms | ||
| AlphaFold2 2.3.1 | Jumper et al.109 and Varadi et al.110 | https://alphafold.ebi.ac.uk/download |
| BEDTools 2.30.0 | Quinlan and Hall111 | https://bedtools.readthedocs.io/en/latest/ |
| BLAT | UCSC Genome Browser | https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads |
| clusterProfiler | Yu et al.112 | https://www.bioconductor.org/packages/release/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html |
| cutadapt 4.4 | Martin113 | https://cutadapt.readthedocs.io/en/stable/ |
| deepTools 3.5.2 | Ramírez et al.114 | https://deeptools.readthedocs.io/en/develop/ |
| DESeq2 1.44 | Love et al.115 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| DEWSeq 1.18.0 | Schwarzl et al.84 | https://bioconductor.org/packages/release/bioc/html/DEWSeq.html |
| g:Profiler | Kolberg et al.116 | https://biit.cs.ut.ee/gprofiler/gost |
| htseq-clip 2.19 | Sahadevan et al.83 | https://htseq-clip.readthedocs.io/en/latest/index.html |
| IHW 1.32.0 | Ignatiadis et al.117 | https://bioconductor.org/packages/3.21/bioc/vignettes/IHW/inst/doc/introduction_to_ihw.html |
| JupyterLab Desktop 4.2.5–1 | Project Jupyter | https://jupyter.org/ |
| MultiQC 1.13 | Ewels et al.118 | https://seqera.io/multiqc/ |
| Python 2.7.15 | Python Software Foundation | https://www.python.org |
| Python 3.8.5 | Python Software Foundation | https://www.python.org |
| R version 4.3.1 | R Foundation | https://www.r-project.org |
| RStudio Desktop 2025.05.0 | Posit Software, PBC | https://posit.co/ |
| Samtools 1.19.1 | Li et al.119 | http://www.htslib.org/download/ |
| STAR 2.7.6a | Dobin et al.120 | https://github.com/alexdobin/STAR/releases |
| UCSC table browser | UCSC Genome Browser | https://genome.ucsc.edu |
| UMI-tools 1.1.5 | Smith et al.121 | https://umi-tools.readthedocs.io/en/latest/index.html |
| Whippet 1.6.2 | Sterne-Weiler et al.122 | https://github.com/timbitz/Whippet.jl |
| FlowJo software | BD Biosciences, version 10.8.1 | https://www.flowjo.com/solutions/flowjo |
| Cytoscape v3.9.1 | Shannon et al.123 | https://cytoscape.org/ |
| STRING plugin v2.0.1 | Doncheva et al.124 | https://apps.cytoscape.org/apps/stringapp |
| Partek Flow software (version 10.0.23.0531) | N/A | https://www.partek.com/partek-flow/ |
| GraphPad Prism Version 9.0 | GraphPad Software Inc. | https://www.graphpad.com/ |
| Adobe Illustrator v28.4.1 | Adobe | https://www.adobe.com/products/illustrator.html |
| Affinity Designer 2 v2.3.0 | Affinity Designer | https://affinity.serif.com/en-us/designer/ |
| BioRender | BioRender | https://www.biorender.com/ |
| Other | ||
| UV Crosslinker | VWR | Cat#89131–484 |
| 4150 TapeStation System | Agilent | Cat#G2992AA |
| BTX Gemini Electroporator | BTX | Cat#452042 |
| Bioruptor Plus sonicator | Diagenode | Cat#B01020002 |
| Mini Gel Tank | Life Technologies | Cat#A25977, |
| Mini Blot Module | Life Technologies | Cat#B1000 |
| VeritPro Thermal Cycler | Applied Biosystems | Cat#A48141 |
| CFX96 Touch Real-Time PCR | BioRad | Cat#1855195 |
| NovaSeq X Sequencing System | Illumina | N/A |
| EVOS™ M5000 Imaging System | Invitrogen | Cat#AMF5000 |
| iBright CL1500 Imaging System | Invitrogen | Cat#A44114 |
| Vi-Cell BLU Cell Viability Analyzer | Beckman Coulter | Cat#C19196 |