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11 protocols using isoginkgetin

1

Cell Culture and Treatment Optimization

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U2OS, HeLa and HeLa Luc/Luc-I cells were cultured in low glucose Dulbecco's modified Eagle medium (HyClone, Thermo Scientific, Stockholm, Sweden) supplemented with 10% fetal bovine serum (Gibco, Thermo Scientific, Stockholm, Sweden) and 2.5 μg/ml plasmocin (InvivoGen, Toulouse, France) at 37 °C in a humidified incubator under 5% CO2. Direct repeated-GFP U2OS cells were cultured in high glucose Dulbecco's modified Eagle medium (HyClone) supplemented with 10% fetal bovine serum and 2.5 μg/ml plasmocin at 37 °C in a humidified incubator under 5% CO2. Human GM00730 fibroblasts (Coriell Institute, Camden, NJ, USA) were cultured in minimum essential medium supplemented with 15% fetal bovine serum and 2.5 μg/ml plasmocin at 37 °C in a humidified incubator under 5% CO2.
For treatment, 100 nM pladienolide B (Santa Cruz Biotechnologies, Heidelberg, Germany) or 50 μM isoginkgetin (Merck Millipore, Solna, Sweden) (final concentrations) were added to the culture medium 1–24 h prior to irradiation or harvesting, with the control cells receiving an equal volume of DMSO (Sigma-Aldrich, Stockholm, Sweden) as the volume of isoginkgetin used. Cycloheximide was added directly to the culture medium to give a final concentration of 50 μg/ml.
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2

Meiotic Maturation Regulation Analysis

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For some analyses, oocytes were treated with 100 µM Isoginkgetin (416154, Sigma Aldrich) alone, co-treated with 100 µM Isoginkgetin and 100 nM Reversine (R3904, Sigma Aldrich) or treated with vehicle solvent alone (DMSO) to assess the effects of interference with RNA splicing on meiotic maturation. In other experiments, oocytes were treated with 50 µM Triptolide (T3652, Sigma Aldrich) to gain insight into the role of transcriptional elongation during meiotic maturation. Control group oocytes were incubated in media containing the appropriate concentration of solvent (DMSO) only under similar conditions. All cultures were maintained at 37°C in MEM/BSA under 5% CO2, 5% O2 and N2. Following culture, oocytes were immediately fixed for immunofluorescence analysis to assess the spindle microtubules, aMTOC components and chromosome configurations.
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3

Cell culture and antibody validation

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Mouse embryonic fibroblasts, HEK 293T and HeLa cells were cultured in DMEM supplemented with 10% fetal calf serum and antibiotics. RPE-1 cells were cultured in DMEM+F12 (1:1) supplemented with 10% fetal calf serum and antibiotics. Antibodies against the mouse Dido amino-terminal region have been described before (35 (link),36 (link)). Antibodies against GST (sc-138, RRID:AB_627677) were from Santa Cruz Biotechnology (Dallas, TX), antibodies against U2AF1 (GTX106854, RRID:AB_1952473) were from Genetex (Irvine, CA) and antibodies against the V5-tag (ab53418, RRID:AB_883403), Tubulin (ab44928, RRID:AB_2241150) SFPQ (ab177149), HNRNPU (ab20666, RRID:AB_732983) and human Dido (ab92868, RRID:AB_10562305) were from Abcam (Cambridge, MA). Actinomycin D (A9415, Sigma, St. Louis, MO) and isoginkgetin (416154, Merck Millipore) were used as described (3 (link),37 (link)). Immunoprecipitation and immunofluorescence were carried out according to standard protocols (36 (link)) as outlined in the Supplementary Data.
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4

Antibody Detection Techniques for Cell Signaling

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Antibodies against C3G (H300, C19), Calnexin, NF-kB, Rap1, and GAPDH were purchased from Santa Cruz Biotechnology. Polyclonal antibody (C9) raised in our laboratory was used to detect C3G specifically (Radha et al., 2007 (link)). Anti-SC35 (S4045-100UL) and anti-­snRNP200 (HPA029321) were from Sigma. Anti-SC35 (ab204916), anti-DHX38 (ab154801), and anti–Lamin B1 (ab16048) were from Abcam. Anti–Flag M2 monoclonal antibody (F3165) was from Sigma. RNA polymerase-II H5 (Warren et al., 1992 (link)) and β-actin antibodies were from Berkeley Antibody Company and Millipore, respectively. U1 snRNP70 (Lerner and Steitz, 1979 (link)), U2 snRNP B″ (Habets et al., 1985 (link)), and Sm snRNP(Y12) (Lerner et al., 1981 (link)) antibodies were gifted by David Spector (Cold Spring Harbor Laboratory [CSHL], Cold Spring Harbor, NY). α-Amanitin, DRB, cytochalacin D, nocadazole, rhodamine-phalloidin, and LiCl were from Sigma. Leptomycin B was from Santa Cruz Biotechnology. Isoginkgetin was from Merck Millipore. Luciferase reagent was from Promega. Lipofectamine 3000 was from Invitrogen. Horseradish peroxidase–conjugated antibodies were from Amersham GE. Fluorophore conjugated secondary antibodies were from Millipore and Amersham GE.
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5

Flavonoid Extraction and Identification

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Hinokiflavone, amentoflavone, cupressuflavone and sciadopitysin were purchased from Extrasynthese (Genay Cedex, France) and isoginkgetin was purchased from MerckMillipore (Darmstadt, Germany).
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6

Proximity Ligation Assay for Ribosomal Protein and β-globin Interaction

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PLA has been described before (15 (link)). H1299 cells were grown on coverslips and transfected with indicated constructs for 24 h and treated with 30 µM isoginkgetin (Merck Millipore) for 22 h. The cells were fixed in 4% paraformaldehyde for 20 min before being permeabilized in PBS and 3% BSA containing 0.1% saponin. PLA was performed with the use of custom-made primary antibodies – rabbit anti-SIIN, goat anti-FEKL (Eurogentec), or rabbit polyclonal antibodies against ribosomal protein L5 (RPL5) were incubated in the same buffer overnight. After the cells were washed, PLA probes were added, followed by hybridization, ligation, and amplification according to the manufacturer’s protocol (Duolink, Thermo Fisher). Then, immunofluorescence was performed using primary mouse anti-β-globin antibody and secondary anti-mouse Alexa488. The coverslips were mounted on slides using SlowFade diamond antifade mounting medium (Thermo Fisher) with Hoescht. PLA signal was analyzed by confocal microscopy followed by full-length β-globin detection by fluorescence microscopy. The number of PLA dots was quantified in H1299 cells with or without β-globin-SL8 immunofluorescence signal by a custom-made automated script in FIJI.
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7

Preparation of Sinefungin and Isoginkgetin Stock Solutions

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Sinefungin was purchased from Enzo Life Sciences (ALX-380-070-M005). A 40 mM Sinefungin stock solution was prepared in DMSO (Sigma-Aldrich, 276855). Lower concentrations were prepared by serial dilution in DMSO and stored at −20 °C until required. Isoginkgetin was purchased from Merck (416154-10) and dissolved at 40 mM in DMSO. Working stocks of 1 mM, 5 mM and 20 mM were prepared by dilution in DMSO.
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8

Tau Exon 10 Alternative Splicing Assay

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The Tau exon 10 alternative splicing
reporter plasmid was courteously provided by the group of Dr. Jane
Y. Wu.11 (link) The HEK293T cells were first transfected
with U1-70K, U1A, or U1C siRNAs for 24 h. At this time point, protein
expressions of these genes were usually suppressed by more than 70%
in preliminary experiments. In the chemical RNA splicing inhibitor
treatment, HEK293T cells were first treated by 33 μM Isoginkgetin
(416154, Merck Millipore) for 12 h. After the U1 knockdown or the
chemical inhibition, the Tau minigene construct prepared in lipofectamine
2000 (ThermoFisher Sicentific) was added to the medium for 24 h before
the enhanced green fluorescent protein (EGFP) expression was examined
and the cells were harvested for qPCR.
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9

H1299 Cell Line Transfection and Treatment

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The human lung carcinoma cell line H1299 was cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS), 2 mM l-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin. Transient transfections were performed using Genejuice reagent (Merck Bioscience) according to manufacturer's protocol. All cells were cultured at 37°C with 5% CO2. For cell treatments with isoginkgetin (Sigma) and PhenDC3 (27 (link)), cells were incubated with 30 and 5 μM of drug for 24 and 40 h after transfection, respectively. Drug stock solutions were prepared in DMSO (Euromedex).
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10

Anti-SARS-CoV-2 N Protein Assay

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Isoginkgetin (MW-566.51 g/mol), % purity ≥ 98% (HPLC) and afzelin (432.38 g/mol), % purity ≥ 90% (LC/MS-UV) were purchased from Sigma-Aldrich, and chloroquine, lopinavir, and remdesivir (used as reference compounds) were bought from Sigma-Aldrich, SelleckChem, and MedChemExpress, respectively. The anti-SARS-CoV-2 N protein antibody was purchased from Sino Biological Inc. (China), with Hoechst-33342 and the Alexa Fluor-488 goat anti-rabbit IgG (H + L) secondary antibody purchased from Molecular Probes. Also, paraformaldehyde (PFA) (a 32% aqueous solution) and normal goat serum were obtained from Vector Laboratories, Inc. (Burlingame, CA) and Electron Microscopy Sciences (Hatfield, PA), respectively. chloroquine was mixed in Dulbecco's Phosphate-Buffered Saline (DPBS; Welgene). For in vitro studies, all reagents were well mixed in DMSO.
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