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9 protocols using mettl14

1

Manipulation of Circular RNA Pathways

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Circular RNA NRIP1, ALKBH5, WTAP, YTHDF1, FTO, METTL3, METTL14, and NC siRNAs were obtained from GenePharma and their sequences are shown in Table S2. The inhibitors and mimics of miRNAs are shown in Table S3. Lipofectamine 3000 (Invitrogen) was used for transfections, following the manufacturer's instructions. A recombinant lentivirus containing sh‐circNRIP1 or sh‐ALKBH5 was established to stably knockdown circNRIP1 or ALKBH5. A nontargeting shRNA was used as the negative control. Circular RNA NRIP1 or ALKBH5 were overexpressed using recombinant lentiviruses containing complete coding sequences of these genes.
An empty lentivirus (vector) was used as the negative control. Lentiviral vectors were constructed by Obio Technologies. Infected cells were selected using puromycin. Quantitative real‐time PCR and immunoblotting were carried out to assess the transfection and infection efficiencies.
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2

Modulating IGF2BP3, SCD, and METTL14 in Cells

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We bought small interfering RNAs (siRNAs) targeting IGF2BP3, SCD, and methyltransferase-like 14 (METTL14) from GenePharma (Shanghai, China). SiRNA and negative control (NC) siRNA was transfected with Lipofectamine 3000 (Invitrogen, USA) ~48 h. qRT-PCR and western blotting were used to verify the transfection efficiency.
Next, the pHBLV-U6-MCS-EF1-Luc-T2A-Puro vector (HANBIO, Shanghai, China) inserted IGF2BP3-shRNA lentivirus, then the lentiviruses-infected CC cells grew in DMEM containing 5 µg/ml polybrene then. IGF2BP3-knockdown cells were transfected with the SCD-overexpression plasmid to rescue. Stable cell lines were produced by selection using 10 µg/ml puromycin (Solarbio, China). The aforesaid sequences appear in Table S1.
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3

siRNA knockdown of key genes in RA-FLSs

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The small interfering RNAs (siRNAs) of IGF2BP2, GSTM5, METTL3 and METTL14 were obtained from GenePharma (Shanghai, China). The sequences are as follows: si-IGF2BP2-1 sense: 5′-GCGAAAGGAUGGUCAUCAUTT-3′; si-IGF2BP2-2 sense: 5′-GCUGUUAACCAACAAGCCATT-3′; si-IGF2BP2-3 sense: 5′-ACAGGACUGUCCGUGCUAUTT-3′; si-GSTM5-1 sense: 5′-GCUGGUCAGACUGUGCUAUTT-3′; si-GSTM5-2 sense: 5′-GGAUUCCUUGCCUAUGAUTT-3′; si-GSTM5-3 sense: 5’-GGGUUUGAAGAAGAUCUCUTT-3′; si-GSTM5-4 sense: 5′-GAAAGUCAGCUACAUGGAATT-3′; si-METTL3 sense: 5′-GCUGCACUUCAGACGAAUUTT-3′; si-METTL14 sense: 5′-GCAGCACCUCGAUCAUUUATT-3′. The siRNAs were transfected into RA-FLSs using a transfection reagent according to the manufacturer’s recommendations. At 6 h after transfection, the medium was replaced with a complete medium. The cells were collected for subsequent experiments at 48 h post-transfection.
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4

Genetic Manipulation of Gastric Cancer Cells

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The normal gastric epithelial cell line GES-1 and GC cell lines (AGS, HGC27, MKN45, and SGC-7901) were purchased from the Cell Bank of the Chinese Academy of Science (Shanghai, China). All cell lines were incubated with RPMI 1640 medium (Solarbio, Beijing, China) supplemented with 10% FBS (Solarbio) in a humidified incubator at 37 °C containing 5% CO2.
FAM120A, WTAP, METTL3, METTL14, YTHDC1, SLCTA11, and PD-L1 knockdown and overexpression lentiviruses and their respective control vectors were generated by GenePharma (Shanghai, China). GC cells were inoculated into 6-well dishes and then infected with lentivirus at 60% confluence. Stable transfected cells were produced by treating cells with puromycin (4 μg/ml) for 2 weeks. The shRNA sequences are listed in Supplementary Table 2.
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5

RNA and Protein Modulation Protocol

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RNase R (20 U/µl, Yeasen) was used to treat total RNA (20 µg) at 37 °C for 15 min. DNA transcription and replication inhibitor actinomycin D (Act D, HY-17,559), protein synthesis inhibitor cycloheximide (CHX, HY-12,320), and vimentin inhibitor Withaferin A (WFA, HY-N2065) were purchased from MedChemExpress (Shanghai, China). SiRNAs targeting ARIH1, vimentin, FTO, METTL3, and METTL14 were purchased from GenePharma (Jiangsu, China).
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6

Knockdown and Overexpression of TRIM9 and METTL14

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Short hairpin (sh)RNA targeting TRIM9 for knockdown (Sh‐TRIM9), shRNA targeting METTL14 for knockdown (METTL14‐KD) and the respective negative controls (NC) (Shanghai GenePharma). The shRNA sequence Sh‐TRIM9 and METTL14‐KD were constructed into the pLVX‐shRNA2‐BSD lentiviral vector (Takara Bio USA, Inc.). Overexpression TRIM9 (Oe‐TRIM9) and overexpression METTL14 (Oe‐TRIM14), lentiviruses (System Biosciences, LLC) were constructed into the lentiviral vector pCDH‐EF1α‐MCS‐T2A‐Puro (System Biosciences, LLC). Cells in each well were transfected with 100 nM miR‐29c‐3p mimic or 200 nM miR‐29c‐3p inhibitor.
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7

RNA Interference Targeting Epigenetic Regulators

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METTL3, METTL14, IGF2BP1/2/3 and IFIT1 small interfering RNAs (siRNAs) were obtained from GenePharma (Shanghai, China). IFIT1 lentivirus shRNAs and pcDNA3.1_IFIT1 overexpressed lentivirus were also obtained from GenePharma (Shanghai, China). The control plasmid, METTL3, METTL14, IFIT1 and PD-L1 overexpressing plasmids were constructed in Generay Technologies (Shanghai, China). Cells were seeded in six-well plates overnight. For siRNA transfection, we made the transfection mixture with 5ul siRNA(50nM), 5ul Dharma FECT 1 transfection reagent and 390ul opti-MEM medium. For plasmid transfection, we added 1ug plasmid and 3ul viaFECT for one well. After six hours of incubation, the medium was replaced by normal culture media. Cells were harvested after 48h. For lentivirus shRNA transfection, cells were incubated with lentivirus at the MOI of 100. After 24 hours’ incubation, cells were treated with puromycin for two weeks. The sequences of siRNAs and shRNAs were listed in Supplementary Table 7.
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8

Silencing HPV and IGF2BP2 in Cervical Cancer

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Small interfering RNAs (siRNAs) targeting HPV16 E6/E7, HPV18 E6/E7, IGF2BP2, and methyltransferase-like 14 (METTL14) were purchased from GenePharma (Shanghai, China). siRNA and negative control (NC) siRNA transfection was performed with Lipofectamine 3000 reagent (Invitrogen, USA) for 48 h. The transfection efficiency was verified by qRT-PCR and western blotting.
The HPV16 E6/E7-shRNA lentivirus, HPV18 E6/E7-shRNA lentivirus, and NC-shRNA were constructed by GenePharma (Shanghai, China). LV17-NC and LV17-Homo IGF2BP2 were cloned into the pcDNA3.1 (+) vector. The CC cells were infected with lentiviruses and cultured in DMEM supplemented with 5 µg/ml polybrene. To rescue the effect of E6/E7 knockdown on CC cells, HPV16/18 E6/E7-knockdown cells were infected with the IGF2BP2-overexpression lentivirus. Stable cell lines were generated by selection with 10 µg/ml puromycin (Solarbio, China). The expression of HPV16 E6/E7, HPV18 E6/E7, and IGF2BP2 was validated by qRT-PCR and western blot. The siRNA, shRNA and plasmid sequences are listed in Table S1.
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9

Modulating m6A Regulators in Cells

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CircNRIP1, ALKBH5, WTAP, YTHDF1, FTO, METTL3, METTL14 and NC siRNAs were obtained from GenePharma (Suzhou, China) and their sequences are shown in Additional le 1 (Table S2).
Lipofectamine 3000 (Invitrogen, Waltham, MA, USA) was used to perform transfections, according to the manufacturer's instructions. A recombinant lentivirus containing sh-circNRIP1 or sh-ALKBH5 was established to stably knock out circNRIP1 or ALKBH5. A non-targeting shRNA (sh-NC) was used as the negative control. circNRIP1 or ALKBH5 were overexpressed using recombinant lentiviruses containing the complete coding sequences of these genes.
An empty lentivirus (vector) was used as the negative control. The lentiviral vectors were constructed by Obio Technologies (Shanghai, China). Infected cells were selected using puromycin. Then, qRT-PCR and immunoblotting were performed to assess the transfection and infection e ciencies.
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