Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-rabbit IgG (H + L)-HRP conjugate (goat) | Biorad | Cat #: 1706516 |
| Anti-GAPDH HRP | Proteintech | Cat #: HRP-60004 |
| anti-HA | Cell Signaling Technology | Cat #: 3724 |
| Anti-SUGP1 | Bethyl Laboratories | Cat #: A304-675A-M |
| Streptavidin, HRP conjugate | Invitrogen | Cat #: S911 |
| Bacterial and virus strains | ||
| NEB® Stable Competent E. coli | New England Biolabs | Cat #: C3040H |
| MegaX DH10B T1R Electrocomp™ Cells | Invitrogen | Cat #: C640003 |
| Escherichia coli BL21 Star (DE3) | Invitrogen | Cat #: C601003 |
| Biological samples | ||
| Chemicals, peptides, and recombinant proteins | ||
| 10-deacetylbaccatin-III (DAB) | Selleckchem | Cat #: S2409 |
| Pladienolide B | Santa Cruz | Cat #: Sc-391691 |
| Biotin | Sigma-Aldrich | Cat #: B4501-500MG |
| Blasticidin | Gibco | Cat #: A1113903 |
| Puromycin | Invivogen | Cat #: ant-pr-1 |
| Transfection reagent: JetPRIME | Polyplus | Cat #: 114-15 |
| SYBR Gold | Invitrogen | Cat #: S11494 |
| NEBuilder® HiFi DNA Assembly | New England Biolabs | Cat #: E2621 |
| NEBnext® Ultra II Q5 Master Mix | New England Biolabs | Cat #: M0544 |
| SuperScript III | Invitrogen | Cat #: 18080093 |
| SuperScript IV | Invitrogen | Cat #: 18090050 |
| MyOne Streptavidin T1 Dynabeads | Invitrogen | Cat #: 65602 |
| Amylose Resin High Flow | New England Biolabs | Cat #: E8022L |
| cOmplete EDTA-free Protease Inhibitor Cocktail | Roche | Cat #: 5056489001 |
| Nicotinamide adenine dinucleotide (NADH) | Carl Roth | Cat #: AE12.1 |
| Phosphoenolpyruvic acid (PEP) | Carl Roth | Cat #: 8397.3 |
| Lactate dehydrogenase (LDH) | Carl Roth | Cat #: 6060.1 |
| Adenosine 5’-Triphosphoric Acid Disodium (ATP) | PanReac AppliChem | Cat #: A1348 |
| Lysozyme | Carl Roth | Cat #: 8259.3 |
| DNase I | PanReac AppliChem | Cat #: 10027460 |
| Critical commercial assays | ||
| CellTiter 96® AQueous One Solution Cell Proliferation Assay | Promega | Cat #: G3582 |
| RNAqueous™-96 Total RNA Isolation Kit | Thermo Fisher | Cat #: AM1920 |
| Poly(A) RNA Selection Kit V1.5 | Lexogen | Cat #: 157.96 |
| CORALL Total RNA-Seq Library Prep Kit with UDI12 nt Set A1 | Lexogen | Cat #: 117.96 |
| PCR Add-on Kit for Illumina | Lexogen | Cat #: 020.96 |
| QuantiFluor RNA System | Promega | Cat #: E3310 |
| Quick Extract DNA Extraction solution | Lucigen | Cat #: QE09050 |
| QIAmp DNA Blood Maxi Kit | Qiagen | Cat #: 51194 |
| Agencourt AMPure XP | Beckman Coulter | Cat #: A63882 |
| RNeasy Plus Mini Kit | Qiagen | Cat #: 74134 |
| BCA protein assay | Thermo Scientific | Cat #: 23227 |
| TMTPro™-16 label plex kit | Thermo Scientific | Cat #: A44521 |
| Deposited data | ||
| All sequencing data (screen, validation, RNA-seq) | This study | GEO: GSE218307 |
| Proximity labeling proteomics data | This study | PRIDE: PXD038067 |
| Human reference genome NCBI guild 38, GRCh38 | Genome Reference Consortium | https://www.ncbi.nlm.nih.gov/grc/human |
| Protein structure: SF3b core with splicing modulator | Cretu et al., 2018 | PDB: 6EN4 |
| Protein structure: substrate-bound A-like U2 snRNP | Tholen et al., 2022 | PDB: 7Q4O |
| Protein structure: chimeric peptide SF3A1 SURP and SF1 | Nameki et al., 2022 | PDB: 7VH9 |
| Protein structure: human Bact spliceosome core | Haselbach et al., 2018 | PDB: 6FF7 |
| Protein structure: human C* spliceosome core | Zhang et al., 2017 | PDB: 5XJC |
| Protein structure: human SUGP1 433/586 | Zhang et al., 2022 | PDB: 8GXM |
| Protein structure: DHX15 in complex with SUGP1 G-patch | Zhang et al., 2022 | PDB: 8EJM |
| Protein structure: DHX15 in complex with NKRF G-patch | Studer et al., 2020 | PDB: 8SH7 |
| Experimental models: Cell lines | ||
| Human: fully-haploid engineered HAP1 (eHAP) wild-type | Horizon Discovery Ltd. | Cat #: C669 |
| Human: eHAP FNLS (and derivatives thereof) | This study | N/A |
| Human: HEK 293T (for lentivirus production) | ATCC | Cat #: CRL-3216 |
| High Five Cells (for protein production) | Gibco | Cat #: B85502 |
| Sf9 cells (for baculovirus production) | Gibco | Cat #: 11496015 |
| Experimental models: Organisms/strains | ||
| Oligonucleotides | ||
| See Table S3 | This study | N/A |
| 5’-6-fluorescein amidites (FAM)-U12 | Microsynth | N/A |
| Recombinant DNA | ||
| pMP783 (pLibrary) | Boettcher et al., 2019 | N/A |
| pLenti-FNLS-P2A-GFP-PGK-Puro | Zafra et al., 2018 | Addgene #110869 |
| pFNLS | This study | N/A |
| p3xFLAG-CMV-14_3xHA_SUGP1 | Zhang et al., 2019a | N/A |
| p3xFLAG-CMV-14_3xHA_SUGP1 E554K | This study | N/A |
| p3xFLAG-CMV-14_3xHA_SUGP1 L570E | This study | N/A |
| p3xFLAG-CMV-14_3xHA_SUGP1 G603N | This study | N/A |
| p3xFLAG-CMV-14_3xHA_SUGP1 Δ αH4-5 | This study | N/A |
| p3xFLAG-CMV-14_3xHA_SUGP1 Δ αH6 | This study | N/A |
| pCDNA3_3xHA-miniTurbo-NLS | Branon et al., 2018 | Addgene #107172 |
| pCDNA3_3xHA-SUGP1-wt-miniTurbo-NLS | This study | N/A |
| pCDNA3_3xHA-SUGP1-L570E-miniTurbo-NLS | This study | N/A |
| pCDNA3_3xHA-SUGP1-G603N-miniTurbo-NLS | This study | N/A |
| psPAX2 (for lentivirus production) | N/A | Addgene #12260 |
| pMD2.G (for lentivirus production) | N/A | Addgene #12259 |
| pFastBac-NpH-DHX15ΔN | Studer et al., 2020 | N/A |
| pnEA-NpH-MBP | Haffke et al., 2015 | N/A |
| pnEA-NpM-SUGP1 G-patch (548-611) wt | This study | N/A |
| pnEA-NpM-SUGP1 G-patch (548-611) E554K | This study | N/A |
| pnEA-NpM-SUGP1 G-patch (548-611) L570E | This study | N/A |
| pnEA-NpM-SUGP1 G-patch (548-611) G603N | This study | N/A |
| pnEA-NpM-SUGP1 αH6-α7 (522-633) wt | This study | N/A |
| pnEA-NpM-SUGP1 αH6-α7 (522-633) E554K | This study | N/A |
| pnEA-NpM-SUGP1 αH6-α7 (522-633) L570E | This study | N/A |
| pnEA-NpM-SUGP1 αH6-α7 (522-633) G603N | This study | N/A |
| pnEA-NpM-SUGP1 αH4-α7 (522-633) wt | This study | N/A |
| pnEA-NpM-SUGP1 αH4-α7 (522-633) E554K | This study | N/A |
| pnEA-NpM-SUGP1 αH4-α7 (522-633) L570E | This study | N/A |
| pnEA-NpM-SUGP1 αH4-α7 (522-633) G603N | This study | N/A |
| Software and algorithms | ||
| CHOPCHOP | Labun et al., 2019 | https://chopchop.cbu.uib.no/ |
| CRISPResso2 (v2.1) | Pinello et al., 2016 | https://github.com/pinellolab/CRISPResso2 |
| Ensembl Variant Effect Predictor (Ensembl release 99) | McLaren et al., 2016 | https://useast.ensembl.org/info/docs/tools/vep/index.html |
| BBDuk (v38.94) | BBtools | http://sourceforge.net/projects/bbmap/ |
| DESeq2 (v1.32.0) | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| RSubreads (v2.6.4) | Liao et al., 2019 | https://bioconductor.org/packages/release/bioc/html/Rsubread.html |
| rMATS-turbo (v4.1.2) | Shen et al., 2014 | https://github.com/Xinglab/rmats-turbo |
| MAJIQ (v2.4) | Mehmood et al., 2020 | https://majiq.biociphers.org/ |
| STAR (v2.7.9) | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| Samtools (v1.10) | Danecek et al., 2021 | https://github.com/samtools/samtools |
| IGV (v2.12.2) | Robinson et al., 2011 | https://software.broadinstitute.org/software/igv/ |
| R (v4.1.2) | The R Project | https://www.r-project.org/ |
| R Studio | R Studio | https://github.com/rstudio/rstudio |
| Prism (v8) | GraphPad Software | https://www.graphpad.com/features |
| FlowJo (v10.8.1) | TreeStar Inc. | https://www.flowjo.com/ |
| PyMOL (v2.3.5) | Schroödinger | https://www.schrodinger.com/products/pymol |
| JalView (v2.11.2.5) | Waterhouse et al., 2009 | https://www.jalview.org/ |
| ImageJ (v1.53) | Schneider et al., 2012 | https://imagej.nih.gov/ij/download.html |
| Other | ||
| Superdex 200 Increase 10/300 GL | Cytiva | Cat #: 28990944 |