Additional file 1 of EIF4A3-induced Circ_0001187 facilitates AML suppression through promoting ubiquitin-proteasomal degradation of METTL3 and decreasing m6A modification level mediated by miR-499a-5p/RNF113A pathway
Creators: name: Yang, Xinyu
name: Han, Fengjiao
name: Hu, Xiang
name: Li, Guosheng
name: Wu, Hanyang
name: Can, Can
name: Wei, Yihong
name: Liu, Jinting
name: Wang, Ruiqing
name: Jia, Wenbo
name: ji, Chunyan
name: Ma, Daoxin
Publisher: name: figshare
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Mental Health
subject: Hematology

description: Additional file 1: Supplementary Figure 1. Expression levelsof different circRNA in patients.Expression levels of Circ_0001187 in AML cell lines. The expressions of Circ_0011929 and Circ_0000973 in AML patients and healthy controls.Relative expression of Circ_0001187 in gender was measured by qRT-PCR.Expression levels of Circ_0001187 and linear DOPEY2 mRNA in THP-1 cellsafter being treated with RNase R by qRT-PCR. Data were analyzed using Unpairedt-test.Expression levels of Circ_0001187 and linearDOPEY2 mRNA in Molm-13 AML cells treated with actinomycin D by qRT-PCR. The qRT-PCR expression results of Circ_0001187 and DOPEY2 using randomprimer and Oligo dT primer in Molm-13 AML cells. The qRT-PCR analysis of nuclear and cytoplasmic fractionation extractsin THP-1 andMolm-13 AML cells. The results of RNA FISH by using sense probein THP-1 and Molm-13 AML cells. **p &lt; 0.01; ****p &lt; 0.0001;ns: Not significant. Supplementary Figure 2. The qRT-PCR results of Circ_0001187 in THP-1 and Molm-13 cells withCirc_0001187 knockdown or overexpression. The proliferation results of THP-1 cellstransfected si-Circ1 or si-Circ 2 by EDU staining. The expression levelof differential genes by RNA-seq analysis.KEGG pathways in Circ_0001187 knockdown compared to the control group.GSEA analysis for Circ_0001187 knockdown compared to the controlgroup. *p &lt; 0.05; **p &lt; 0.01; ***p &lt; 0.001; ****p &lt; 0.0001. Supplementary Figure 3. The qRT-PCR results of Circ_0001187 in mice treatedwith sh-Circ compared with negative control. The spleen weight of AML mice injectedwith THP-1 cells transfected with sh-Circ_0001187-GFP or Ctrl-GFP.Differential expression of miRNA from RNA pull-down.miRNA and target mRNA predictionnetwork of Circ_0001187 via RNA pulldown assay. The results of GO enrichment correspond tomiRNA/mRNA. *p &lt; 0.05; ***p &lt; 0.001. Supplementary Figure 4. The results of coomassie blue staining inTHP-1with Circ_0001187 knockdown. The protein METTL3 identified by mass spectrometryanalysis. The qRT-PCR results of METTL3 in THP-1 and Molm-13 AML cells with Circ_0001187 knockdown.Western blot results of METTL3 in 293-T cells treated with 20 μg/ml CHX at different times. The mRNA leve of MYB, MYC and ITGA4 in THP-1and Molm-13AML cells with Circ_0001187 knockdown. The potential METTL3 E3 ligases identifiedby affinity MS.Western blot results of METTL3in THP-1 cells transduced with the siRNA of potentialE3 ligases respectively compared with negative control. The expression levels of RNF113A from TCGA database. The proliferation results of THP-1 and Molm-13cells with RNF113A knockdown by CCK-8 assays. The effect of RNF113A knockdown on theapoptosis of THP-1 and Molm-13 cells by flow cytometry. *p &lt; 0.05; **p&lt; 0.01; ***p &lt; 0.001; ****p &lt; 0.0001; ns: Not significant. Supplementary Figure 5. The results of RNA FISH by using sense probe in THP-1 and Molm-13 AML cells. The effect of miR-499a-5p mimics on theproliferation of THP-1 and Molm-13 cells. The effect of miR-499a-5p mimics onthe apoptosis of THP-1 and Molm-13 cells.ChIP‒qPCR showingthe effect of chidamide on the histoneacetylation levels of Circ_0001187 by promoters in THP-1 and Molm-13 cells. TheRNA-bing protein sites matching flanking regions of circRNA from Circintercomedatabase. The results from RBPsuit database. The expression levels of EIF4A3 from TCGAdatabase. The effect of oe-EIF4A3or oe-EIF4A3/siCirc on the proliferation of THP-1 cells. The effect of oe-EIF4A3 or oe-EIF4A3/siCircon the apoptosis of THP-1 cells. *p &lt; 0.05; **p &lt;0.01; ***p &lt; 0.001; ****p&lt; 0.0001; ns: Not significant. Supplementary Table 1. Risk classification standard. Supplementary Table 2. Primers used for quantitative reversetranscription PCR. Supplementary Table 3. The sequences for oligonucleotide transfection. Supplementary Table 4. Primer sets for MSP and CHIP