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8 protocols using 1 na pp1

1

Transcriptional Regulation in HEK293 and HeLa Cells

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HEK293 and HeLa cells were obtained from ATCC (ATCC® CRL‐1573™ and ATCC® CCL‐2™, respectively). HeLa, HEK293 parental cells, and CDK9as HEK293 cells were grown in DMEM medium supplemented with 10% fetal calf serum, 100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L‐glutamine at 37°C and 5% CO2. HEK293 and CDK9as cells were treated with 7.5, 10, or 15 μM 1‐NA‐PP1 (Cayman Chemical Company) for 15 and 30 min. HEK293, CDK9as, or HeLa cells were treated with 10 ng/ml of TNFα (PeproTech), 2.5 nM Calyculin A (Sigma), 25 nM Tautomycetin (Bio‐Techne), 2.5 nM LB‐100 (Stratech Scientific Ltd), 100 μM DRB (Sigma) for 5, 10, 15, or 30 min. As a negative control, HEK293, CDK9as, and HeLa cells were treated with DMSO (the resuspension vehicle for NA, DRB, Calyculin A, LB‐100, and Tautomycetin). Cells were routinely checked to be free of mycoplasma contamination using Plasmo Test Mycoplasma Detection Kit (InvivoGen, rep‐pt1).
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2

Mitochondrial Function Modulation in Cell Lines

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HEK293T cells were obtained from ATCC. HeLa cells were a gifted by Sabrina Spencer. Beige fat cells were a gift from Shingo Kajimura. Cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal calf serum (Invitrogen), penicillin, streptomycin (100units/mL), and 1 mM L-glutamine. Cells were treated at indicated concentrations with CCCP (SigmaAldrich), valinomycin (Tocris), Antimycin (SigmaAldrich) Oligomycin (Cayman Chemical), Actinonin (Cayman Chemical), FK506 (Cayman Chemical), 1-NA-PP1 (Cayman Chemical), Bafilomycin A1 (SigmaAldrich), and Ru360 (EMDMillipore). Antibodies were purchased from the following providers: anti-PDH, Abcam; anti-Tom20, Proteintech. Fluorescent labeled secondary antibodies were purchased from ThermoFisher.
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3

Analog-Sensitive Kinase Inhibition

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For strains containing cdk1–as, the kinase was inhibited with 10 µM 1–NM–PP1 (Toronto Research Chemicals, A603003). For strains containing ime2–as, the kinase was inhibited with 20 µM 1–NA–PP1 (Cayman Chemical Co., NC1049860). For experiments comparing the effects of inhibiting one or both kinases, both inhibitors were added to each strain regardless of genotype to normalize for the effect of the inhibitor without the corresponding analog–sensitive allele. Both inhibitors were prepared from 20 mM stocks in DMSO.
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4

Meiosis Induction and Synchronization

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Meiosis was induced at 30°C (Arguello‐Miranda et al, 2017 (link)). Briefly, respiration‐competent cells grown on YPD medium for 24 h were evenly spread on YPD plates and allowed to form a lawn (24 h). Cells were inoculated (OD600 = 0.3; 5 × 106 cells/ml) into liquid YPA medium (YP plus 2% K‐acetate) and grown for 12 h until entry into a transient G1 arrest. Cells were washed with sporulation medium (SPM, 2% K‐acetate), inoculated (OD600 = 2.4) into 100 ml of SPM in a 2.8 l‐Fernbach flask, and rotated on an orbital shaker (200 rpm). PEST‐NDT80 PHSL1‐CDC20 cells were released into metaphase I with estradiol (5 μM) at 7 h in SPM, and CDC20‐mAR cells were released into anaphase I with CuSO4 (10 μM) at 8 h in SPM. Kinases were inhibited with 1NM‐PP1 (Cayman Chemical; Cdk1‐as1 and Hrr25‐as, 5 μM), 1Na‐PP1 (Cayman Chemical; Cdk1‐as2, 10 μM; Ime2‐as, 20 μM), or CMK (MedChemExpress; Cdc5‐as, 20 μM). The auxin analogue 5‐Ph‐IAA (BioAcademia, Osaka, Japan) was used at 0.1 mM and cycloheximide at 0.5 mg/ml.
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5

Conditional Protein Depletion in Meiosis

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The anchor away technique was used to conditionally deplete proteins from the nucleus upon addition of rapamycin [37 (link)]. Rapamycin was added at a final concentration of 1 μM to the meiotic cultures at either meiotic induction (T = 0 h) or during pachynema (T = 6 h) except for depletion of Spo11-FRB or Mer2-FRB, where 2 μM rapamycin was added to the cells. mek1-as1 [60 (link)] was conditionally inactivated by addition of the ATP analog, 1-NA-PP1 (Cayman Chemicals), at a final concentration of 2 μM, to the meiotic cultures during pachynema (T = 6 h).
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6

Mitochondrial Function Modulation in Cell Lines

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HEK293T cells were obtained from ATCC. HeLa cells were a gifted by Sabrina Spencer. Beige fat cells were a gift from Shingo Kajimura. Cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal calf serum (Invitrogen), penicillin, streptomycin (100units/mL), and 1 mM L-glutamine. Cells were treated at indicated concentrations with CCCP (SigmaAldrich), valinomycin (Tocris), Antimycin (SigmaAldrich) Oligomycin (Cayman Chemical), Actinonin (Cayman Chemical), FK506 (Cayman Chemical), 1-NA-PP1 (Cayman Chemical), Bafilomycin A1 (SigmaAldrich), and Ru360 (EMDMillipore). Antibodies were purchased from the following providers: anti-PDH, Abcam; anti-Tom20, Proteintech. Fluorescent labeled secondary antibodies were purchased from ThermoFisher.
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7

PLK4-Mediated Tubulin Recruitment Assay

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PLK4 assemblies were formed by adding purified GFP–PLK4 (1 µM) to the condensate buffer (150 mM NaCl, 25 mM HEPES pH 7.4 and 1 mM DTT). PLK4 was incubated for 5 to 10 min at room temperature (or at different temperatures when checking their effect on PLK4 assemblies; Fig. S2C) and then imaged using a spinning disc CSU-X1 (Yokogawa) confocal scan head coupled to a Nikon Eclipse Ti-E and controlled using MetaMorph 7.5 (Molecular Devices). For tubulin recruitment, Rhodamine–TRITC-labelled tubulin (Cytoskeleton; 500 nM) was added to the condensate buffer. We used BRB80 buffer (see below) as a control. For the experiments using inactive PLK4, 1NA-PP1 (Cayman Chemical, CAYM10954-1, 100 µM) was used to inactivate PLK4AS; DMSO was used as a control. Dephosphorylation of PLK4 was performed using the typical reaction protocol for λ-phosphatase, incubated for 1 h at room temperature and processed either for confocal imaging or for electron microscopy. A sample was taken to check for PLK4 activity by western blotting using a rabbit antibody against phosphorylated threonine-170 raised in our laboratory (see below).
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8

Studying CDK9 Inhibition in HEK293 and HeLa Cells

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Cell culture HEK293 and HeLa cells were obtained from ATCC (ATCC® CRL-1573™ and ATCC® CCL-2™, respectively). HeLa, HEK293 parental cells, and CDK9as HEK293 cells were grown in DMEM medium supplemented with 10% foetal calf serum, 100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine at 37°C and 5% CO 2 . HEK293 and CDK9as cells were treated with 7.5, 10, or 15 μM 1-NA-PP1 (Cayman Chemical Company) for 15 and 30 minutes. HEK293, CDK9as, or HeLa cells were treated with 10 ng/ml of TNFα (PeproTech), Chromatin immunoprecipitation (ChIP)
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