human embryonic kidney stromal cell line hek293t  (ATCC)


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    ATCC human embryonic kidney stromal cell line hek293t
    Human Embryonic Kidney Stromal Cell Line Hek293t, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    human embryonic kidney epithelial hek293t cell line  (ATCC)


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    ATCC human embryonic kidney epithelial hek293t cell line
    Human Embryonic Kidney Epithelial Hek293t Cell Line, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    human embryonic kidney cell line hek293t  (ATCC)


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    ATCC human embryonic kidney cell line hek293t
    See also Extended Data Fig. 4. (a) Heatmap of miRNA expression in A549-Ctrl and A549-N cells based on small RNA sequencing. (b) Quantification of five miRNAs in A549-Ctrl and A549-N cells. (c) Ratio of cytosolic pre-miRNA levels to nuclear pre-miRNA levels in A549-Ctrl and A549-N cells. (d) Ratio of cytosolic pre-miRNA levels to nuclear pre-miRNA levels in A549-Ctrl and A549-N cells transfected with a plasmid expressing XPO5 or control plasmid. (e) Ratio of mature miRNA levels to pre-miRNA levels in A549-Ctrl and A549-N cells. (f) Ratio of mature miRNA levels to pre-miRNA levels in A549-Ctrl and A549-N cells transfected with a plasmid expressing Dicer or control plasmid. (g) miRNA levels in A549-Ctrl or A549-N cells co-transfected with XPO5-expressing and Dicer-expressing plasmids. (h) Luciferase assay of <t>HEK293T</t> cells following co-transfection of splicing reporter with SRSF3-specific siRNA (siSRSF3), hnRNPA3-specific siRNA (sihnRNPA3), or control siRNA. (i) Luciferase assay of HEK293T-Ctrl or HEK293T-N cells following co-transfection of splicing reporter with SRSF3-expressing, hnRNPA3-expressing, or control plasmids. (j) Changes in percent spliced-in (PSI) values between A549-Ctrl and A549-N cells determined using full-length transcriptome sequencing data. ΔPSI = PSI(A549-N) − PSI(A549-Ctrl). (k) Relative fraction of transcripts with intron retention over total sequencing reads determined using full-length transcriptome sequencing data. (l) Relative intronic and exonic RNA levels of the indicated genes in A549-Ctrl and A549-N cells. (m) Relative intronic and exonic RNA levels of the indicated genes in A549-Ctrl and A549-N cells co-transfected with SRSF3-expressing and hnRNPA3-expressing plasmids. Data in b–i and k–m are expressed as mean ± SD of three biological replicates. **p < 0.01; *p < 0.05; ns, not significant (p > 0.05; two-sided Student’s t -test). Ctrl: control plasmid; N: N protein; siNC: negative control siRNA; SES: single exon skipping; MES: multiple exon skipping; MXE: mutually exclusive exons; A5SS or A3SS: alternative 5′ and 3′ splice sites, respectively; IR: intron retention.
    Human Embryonic Kidney Cell Line Hek293t, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "SARS-CoV-2 N protein-induced Dicer, XPO5, SRSF3, and hnRNPA3 downregulation causes pneumonia"

    Article Title: SARS-CoV-2 N protein-induced Dicer, XPO5, SRSF3, and hnRNPA3 downregulation causes pneumonia

    Journal: bioRxiv

    doi: 10.1101/2023.10.03.560426

    See also Extended Data Fig. 4. (a) Heatmap of miRNA expression in A549-Ctrl and A549-N cells based on small RNA sequencing. (b) Quantification of five miRNAs in A549-Ctrl and A549-N cells. (c) Ratio of cytosolic pre-miRNA levels to nuclear pre-miRNA levels in A549-Ctrl and A549-N cells. (d) Ratio of cytosolic pre-miRNA levels to nuclear pre-miRNA levels in A549-Ctrl and A549-N cells transfected with a plasmid expressing XPO5 or control plasmid. (e) Ratio of mature miRNA levels to pre-miRNA levels in A549-Ctrl and A549-N cells. (f) Ratio of mature miRNA levels to pre-miRNA levels in A549-Ctrl and A549-N cells transfected with a plasmid expressing Dicer or control plasmid. (g) miRNA levels in A549-Ctrl or A549-N cells co-transfected with XPO5-expressing and Dicer-expressing plasmids. (h) Luciferase assay of HEK293T cells following co-transfection of splicing reporter with SRSF3-specific siRNA (siSRSF3), hnRNPA3-specific siRNA (sihnRNPA3), or control siRNA. (i) Luciferase assay of HEK293T-Ctrl or HEK293T-N cells following co-transfection of splicing reporter with SRSF3-expressing, hnRNPA3-expressing, or control plasmids. (j) Changes in percent spliced-in (PSI) values between A549-Ctrl and A549-N cells determined using full-length transcriptome sequencing data. ΔPSI = PSI(A549-N) − PSI(A549-Ctrl). (k) Relative fraction of transcripts with intron retention over total sequencing reads determined using full-length transcriptome sequencing data. (l) Relative intronic and exonic RNA levels of the indicated genes in A549-Ctrl and A549-N cells. (m) Relative intronic and exonic RNA levels of the indicated genes in A549-Ctrl and A549-N cells co-transfected with SRSF3-expressing and hnRNPA3-expressing plasmids. Data in b–i and k–m are expressed as mean ± SD of three biological replicates. **p < 0.01; *p < 0.05; ns, not significant (p > 0.05; two-sided Student’s t -test). Ctrl: control plasmid; N: N protein; siNC: negative control siRNA; SES: single exon skipping; MES: multiple exon skipping; MXE: mutually exclusive exons; A5SS or A3SS: alternative 5′ and 3′ splice sites, respectively; IR: intron retention.
    Figure Legend Snippet: See also Extended Data Fig. 4. (a) Heatmap of miRNA expression in A549-Ctrl and A549-N cells based on small RNA sequencing. (b) Quantification of five miRNAs in A549-Ctrl and A549-N cells. (c) Ratio of cytosolic pre-miRNA levels to nuclear pre-miRNA levels in A549-Ctrl and A549-N cells. (d) Ratio of cytosolic pre-miRNA levels to nuclear pre-miRNA levels in A549-Ctrl and A549-N cells transfected with a plasmid expressing XPO5 or control plasmid. (e) Ratio of mature miRNA levels to pre-miRNA levels in A549-Ctrl and A549-N cells. (f) Ratio of mature miRNA levels to pre-miRNA levels in A549-Ctrl and A549-N cells transfected with a plasmid expressing Dicer or control plasmid. (g) miRNA levels in A549-Ctrl or A549-N cells co-transfected with XPO5-expressing and Dicer-expressing plasmids. (h) Luciferase assay of HEK293T cells following co-transfection of splicing reporter with SRSF3-specific siRNA (siSRSF3), hnRNPA3-specific siRNA (sihnRNPA3), or control siRNA. (i) Luciferase assay of HEK293T-Ctrl or HEK293T-N cells following co-transfection of splicing reporter with SRSF3-expressing, hnRNPA3-expressing, or control plasmids. (j) Changes in percent spliced-in (PSI) values between A549-Ctrl and A549-N cells determined using full-length transcriptome sequencing data. ΔPSI = PSI(A549-N) − PSI(A549-Ctrl). (k) Relative fraction of transcripts with intron retention over total sequencing reads determined using full-length transcriptome sequencing data. (l) Relative intronic and exonic RNA levels of the indicated genes in A549-Ctrl and A549-N cells. (m) Relative intronic and exonic RNA levels of the indicated genes in A549-Ctrl and A549-N cells co-transfected with SRSF3-expressing and hnRNPA3-expressing plasmids. Data in b–i and k–m are expressed as mean ± SD of three biological replicates. **p < 0.01; *p < 0.05; ns, not significant (p > 0.05; two-sided Student’s t -test). Ctrl: control plasmid; N: N protein; siNC: negative control siRNA; SES: single exon skipping; MES: multiple exon skipping; MXE: mutually exclusive exons; A5SS or A3SS: alternative 5′ and 3′ splice sites, respectively; IR: intron retention.

    Techniques Used: Expressing, RNA Sequencing Assay, Transfection, Plasmid Preparation, Luciferase, Cotransfection, Sequencing, Negative Control

    human embryonic kidney hek293t cell line  (ATCC)


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    ATCC human embryonic kidney hek293t cell line
    Human Embryonic Kidney Hek293t Cell Line, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    human embryonic kidney hek293t cell line  (ATCC)


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    ATCC human embryonic kidney hek293t cell line
    iM- and G4-CUT&Tag efficiency among replicates. ( A ) Peak width distribution; top: <t>HEK293T</t> iM/G4-CUT&Tag samples; bottom: WDLPS iM/G4-CUT&Tag samples. ( B ) Visualization of representative genomic regions of iM- (yellow) and G4- (blue) CUT&Tag tracks in HEK293T (left) and WDLPS (right) cell lines. Reads were aligned to the human genome (hg38) and normalized by reads per million. SEACR-identified peaks for the three biological replicates (R) are shown below each peak as colored boxes (yellow for iM and blue for G4 samples). Gene annotation, when available, is reported at the bottom of the track. Representative peaks present in both iM- and G4-CUT&Tag samples (top), or unique peaks present in only one of the two sets are shown (middle and bottom). ( C ) FRiP generated for iM- and G4-CUT&Tag samples from both HEK293T and WDLPS cell lines. Error bars represent standard deviations of three independent replicates.
    Human Embryonic Kidney Hek293t Cell Line, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/human embryonic kidney hek293t cell line/product/ATCC
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    1) Product Images from "Genome-wide mapping of i-motifs reveals their association with transcription regulation in live human cells"

    Article Title: Genome-wide mapping of i-motifs reveals their association with transcription regulation in live human cells

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkad626

    iM- and G4-CUT&Tag efficiency among replicates. ( A ) Peak width distribution; top: HEK293T iM/G4-CUT&Tag samples; bottom: WDLPS iM/G4-CUT&Tag samples. ( B ) Visualization of representative genomic regions of iM- (yellow) and G4- (blue) CUT&Tag tracks in HEK293T (left) and WDLPS (right) cell lines. Reads were aligned to the human genome (hg38) and normalized by reads per million. SEACR-identified peaks for the three biological replicates (R) are shown below each peak as colored boxes (yellow for iM and blue for G4 samples). Gene annotation, when available, is reported at the bottom of the track. Representative peaks present in both iM- and G4-CUT&Tag samples (top), or unique peaks present in only one of the two sets are shown (middle and bottom). ( C ) FRiP generated for iM- and G4-CUT&Tag samples from both HEK293T and WDLPS cell lines. Error bars represent standard deviations of three independent replicates.
    Figure Legend Snippet: iM- and G4-CUT&Tag efficiency among replicates. ( A ) Peak width distribution; top: HEK293T iM/G4-CUT&Tag samples; bottom: WDLPS iM/G4-CUT&Tag samples. ( B ) Visualization of representative genomic regions of iM- (yellow) and G4- (blue) CUT&Tag tracks in HEK293T (left) and WDLPS (right) cell lines. Reads were aligned to the human genome (hg38) and normalized by reads per million. SEACR-identified peaks for the three biological replicates (R) are shown below each peak as colored boxes (yellow for iM and blue for G4 samples). Gene annotation, when available, is reported at the bottom of the track. Representative peaks present in both iM- and G4-CUT&Tag samples (top), or unique peaks present in only one of the two sets are shown (middle and bottom). ( C ) FRiP generated for iM- and G4-CUT&Tag samples from both HEK293T and WDLPS cell lines. Error bars represent standard deviations of three independent replicates.

    Techniques Used: Generated

    iM- and G4-CUT&Tag sequencing results. ( A ) Donut charts representing the distribution of high-confidence peaks for both iM- and G4-samples from HEK293T (upper charts) and WDLPS (lower graphs) in functional genomic regions, according to ChIPseeker annotation. The percentages are normalized over the genomic abundance of each functional region and numeric values are reported in the legend for each sample. ( B ) Average plot (top) and density heatmaps (bottom) of G4- and iM-CUT&Tag peaks in HEK293T (left) and WDLPS (right). For each cell line, peak density is referred to the TSS within ±1 kb distance, and the corresponding H3K4me3-CUT&Tag density profile is shown on the right. ( C ) Investigation of recurrent motifs research using MEME-ChIP from the high confidence iM- and G4-CUT&Tag peaks. For each sample, two motifs with their E -value are reported. ( D ) Visualization tracks of iM-CUT&Tag profiles, referred to known iM-forming sequences in vitro . Reads were aligned to the human genome hg38 and normalized to reads per million. SEACR-identified peaks are shown as colored boxes below each peak. Gene annotation is reported at the bottom of each track. ( E ) Percentages of putative iM- and G4-forming sequences normalized on total peaks (pie charts) and fold enrichment (bar chart), relative to randomly composed sequences (average of 10 randomizations per sequence) in HEK293T (top) and WDLPS (bottom). Plain bars indicate iM-forming sequences, pattern-filled bars indicate G4-forming sequences. iM/G4 prediction was performed for the following motifs: low stringency , four C/G-tracts with at least two Cs/Gs each; medium stringency , four C/G-tracts with at least three Cs/Gs each; high stringency , five C/G-tracts with at least three Cs/Gs each. For each searching motif, two loop sizes, short (0–7) and long (0–12), were evaluated. The dashed line indicates fold enrichment = 1. ( F ) CD spectroscopy analysis of representative identified CC-, CCC- and CCCC-tract piMs in HEK293T (top) and WDLPS (bottom). Oligonucleotides were folded in phosphate buffer and analyzed at different pH levels, as indicated.
    Figure Legend Snippet: iM- and G4-CUT&Tag sequencing results. ( A ) Donut charts representing the distribution of high-confidence peaks for both iM- and G4-samples from HEK293T (upper charts) and WDLPS (lower graphs) in functional genomic regions, according to ChIPseeker annotation. The percentages are normalized over the genomic abundance of each functional region and numeric values are reported in the legend for each sample. ( B ) Average plot (top) and density heatmaps (bottom) of G4- and iM-CUT&Tag peaks in HEK293T (left) and WDLPS (right). For each cell line, peak density is referred to the TSS within ±1 kb distance, and the corresponding H3K4me3-CUT&Tag density profile is shown on the right. ( C ) Investigation of recurrent motifs research using MEME-ChIP from the high confidence iM- and G4-CUT&Tag peaks. For each sample, two motifs with their E -value are reported. ( D ) Visualization tracks of iM-CUT&Tag profiles, referred to known iM-forming sequences in vitro . Reads were aligned to the human genome hg38 and normalized to reads per million. SEACR-identified peaks are shown as colored boxes below each peak. Gene annotation is reported at the bottom of each track. ( E ) Percentages of putative iM- and G4-forming sequences normalized on total peaks (pie charts) and fold enrichment (bar chart), relative to randomly composed sequences (average of 10 randomizations per sequence) in HEK293T (top) and WDLPS (bottom). Plain bars indicate iM-forming sequences, pattern-filled bars indicate G4-forming sequences. iM/G4 prediction was performed for the following motifs: low stringency , four C/G-tracts with at least two Cs/Gs each; medium stringency , four C/G-tracts with at least three Cs/Gs each; high stringency , five C/G-tracts with at least three Cs/Gs each. For each searching motif, two loop sizes, short (0–7) and long (0–12), were evaluated. The dashed line indicates fold enrichment = 1. ( F ) CD spectroscopy analysis of representative identified CC-, CCC- and CCCC-tract piMs in HEK293T (top) and WDLPS (bottom). Oligonucleotides were folded in phosphate buffer and analyzed at different pH levels, as indicated.

    Techniques Used: Sequencing, Functional Assay, In Vitro, Spectroscopy

    iM and G4s distribution and possible biological role. ( A ) Venn diagrams showing shared and unique peaks from iM- and G4-CUT&Tag analyses in HEK293T (left) and WDLPS (right). ( B ) Donut plots showing the distribution of shared and unique peaks in HEK293T (top) and WDLPS (bottom) in functional genomic regions, according to ChIPseeker annotation. Percentages are normalized over the genomic abundance of each functional region, and numerical values are reported in the legend for each sample. ( C ) Reactome pathway enrichment analysis of top iM-peaks annotated to TSS from HEK293T cells. The top 10 most over-represented pathways are listed by P -value and their colors indicate the number of genes found. P -value < 0.001. UPR: Unfolded Protein Response; NMD: Nonsense-Mediated Decay; EJC: Exon Junction Complex.
    Figure Legend Snippet: iM and G4s distribution and possible biological role. ( A ) Venn diagrams showing shared and unique peaks from iM- and G4-CUT&Tag analyses in HEK293T (left) and WDLPS (right). ( B ) Donut plots showing the distribution of shared and unique peaks in HEK293T (top) and WDLPS (bottom) in functional genomic regions, according to ChIPseeker annotation. Percentages are normalized over the genomic abundance of each functional region, and numerical values are reported in the legend for each sample. ( C ) Reactome pathway enrichment analysis of top iM-peaks annotated to TSS from HEK293T cells. The top 10 most over-represented pathways are listed by P -value and their colors indicate the number of genes found. P -value < 0.001. UPR: Unfolded Protein Response; NMD: Nonsense-Mediated Decay; EJC: Exon Junction Complex.

    Techniques Used: Functional Assay

    iMs association with transcription, open chromatin regions and DNA-RNA hybrid structures. A-B) RNA-seq integration data: gene expression distribution was reported in transcripts per million (TPM) of genes included in iM-unique peaks (right panel) and G4-unique peaks (left panel) from HEK293T ( A ) and WDLPS ( B ). Genes were grouped according to the functional annotation of the immunoprecipitated region. Outliers were excluded with the interquartile range method. C-D) Gene expression distribution of all the expressed genes (at least one transcript per gene) in HEK293T ( C ) and WDLPS ( D ) cells according to RNA-seq data. Three expression categories were defined based on the quartiles of expression distribution: the first quartile corresponds to low expression, the central two quartiles to medium expression and the upper quartile to high expression. The percentage of iM- and G4-containing genes is shown according to their expression level (no, low, medium, or high expression). ( E ) Venn diagrams showing shared peaks between ATAC-seq (green) and iM- (purple) and G4-CUT&Tag reactions (blue). Peak subsets were defined according to ChIPseeker annotation to promoter regions. ( F ) Percentage of iM- (pink) and G4-containing (blue) genes in HEK293T shared with the ATAC-seq dataset, according to their expression level (no, low, medium, or high expression). ( G ) Venn diagrams representing the intersection between R-loop CUT&Tag (orange) and CUT&Tag data (G4-CUT&Tag in blue and iM-CUT&Tag in purple). ( H ) Correlation plots of HEK293T CUT&Tag versus ATAC-seq (left) and versus R-loop CUT&Tag (right). Pearson's correlation values for all samples are reported.
    Figure Legend Snippet: iMs association with transcription, open chromatin regions and DNA-RNA hybrid structures. A-B) RNA-seq integration data: gene expression distribution was reported in transcripts per million (TPM) of genes included in iM-unique peaks (right panel) and G4-unique peaks (left panel) from HEK293T ( A ) and WDLPS ( B ). Genes were grouped according to the functional annotation of the immunoprecipitated region. Outliers were excluded with the interquartile range method. C-D) Gene expression distribution of all the expressed genes (at least one transcript per gene) in HEK293T ( C ) and WDLPS ( D ) cells according to RNA-seq data. Three expression categories were defined based on the quartiles of expression distribution: the first quartile corresponds to low expression, the central two quartiles to medium expression and the upper quartile to high expression. The percentage of iM- and G4-containing genes is shown according to their expression level (no, low, medium, or high expression). ( E ) Venn diagrams showing shared peaks between ATAC-seq (green) and iM- (purple) and G4-CUT&Tag reactions (blue). Peak subsets were defined according to ChIPseeker annotation to promoter regions. ( F ) Percentage of iM- (pink) and G4-containing (blue) genes in HEK293T shared with the ATAC-seq dataset, according to their expression level (no, low, medium, or high expression). ( G ) Venn diagrams representing the intersection between R-loop CUT&Tag (orange) and CUT&Tag data (G4-CUT&Tag in blue and iM-CUT&Tag in purple). ( H ) Correlation plots of HEK293T CUT&Tag versus ATAC-seq (left) and versus R-loop CUT&Tag (right). Pearson's correlation values for all samples are reported.

    Techniques Used: RNA Sequencing Assay, Expressing, Functional Assay, Immunoprecipitation

    cell lines human embryonic kidney hek 293t  (ATCC)


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    ATCC cell lines human embryonic kidney hek 293t
    Cell Lines Human Embryonic Kidney Hek 293t, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    human embryonic kidney 293t hek 293t cell line  (ATCC)


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    ATCC human embryonic kidney 293t hek 293t cell line
    Lnc-PLA2G4A-4 directly binds to miR-23b-3p. A. Fluorescence in Situ Hybridization assay used to examine the expression and location of Lnc-PLA2G4A-4 in SMMC-7721 and SK-Hep-1 cells. B. Cell fractionation assay used to examine the location of Lnc-PLA2G4A-4 in SMMC-7721 and SK-Hep-1 cells. C. The predicted results of Lnc-PLA2G4A-4 downstream target genes from three databases. D. Relative luciferase activities in <t>293T</t> cells co-transfected with the mimic-NC/miR-567 mimic/miR-888 mimic/miR-23b-3p mimic and Lnc-PLA2G4A-4-WT reporter vector. E. Up: prediction of miR-23b-3p binding sites in Lnc-PLA2G4A-4 (Lnc-PLA2G4A-4-WT) and the design of Lnc-PLA2G4A-4 mutation sequence (Lnc-PLA2G4A-4-Mut). Down: luciferase reporter assays were performed in 293T cells co-transfected with the miR-23b-3p mimic and Lnc-PLA2G4A-4-WT or Lnc-PLA2G4A-4-Mut reporter vector. F. Relative expression of miR-23b in different HCC cell lines. G. Expression of miR-23b-3p in 50 normal tissue and 374 HCC tumor tissue from TCGA cohort in Student's unpaired t -test. H. Expression of miR-23b in 49 normal tissue and 49 HCC tumor tissue from TCGA cohort in Student's paired t -test. I. Relative expression of miR-23b in Lnc-PLA2G4A-4 over-expression cells or Lnc-PLA2G4A-4 knockdown cells, respectively. J. Correlation between miR-23b-3p and Lnc-PLA2G4A-4 expression in HCC tissues of MCHH. K. Correlation between miR-23b-3p and Lnc-PLA2G4A-4 expression in HCC tissues of TCGA.
    Human Embryonic Kidney 293t Hek 293t Cell Line, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 86 stars, based on 1 article reviews
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    human embryonic kidney 293t hek 293t cell line - by Bioz Stars, 2023-11
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    1) Product Images from "Lnc-PLA2G4A-4 facilitates the progression of hepatocellular carcinoma by inducing versican expression via sponging miR-23b-3p"

    Article Title: Lnc-PLA2G4A-4 facilitates the progression of hepatocellular carcinoma by inducing versican expression via sponging miR-23b-3p

    Journal: Heliyon

    doi: 10.1016/j.heliyon.2023.e18698

    Lnc-PLA2G4A-4 directly binds to miR-23b-3p. A. Fluorescence in Situ Hybridization assay used to examine the expression and location of Lnc-PLA2G4A-4 in SMMC-7721 and SK-Hep-1 cells. B. Cell fractionation assay used to examine the location of Lnc-PLA2G4A-4 in SMMC-7721 and SK-Hep-1 cells. C. The predicted results of Lnc-PLA2G4A-4 downstream target genes from three databases. D. Relative luciferase activities in 293T cells co-transfected with the mimic-NC/miR-567 mimic/miR-888 mimic/miR-23b-3p mimic and Lnc-PLA2G4A-4-WT reporter vector. E. Up: prediction of miR-23b-3p binding sites in Lnc-PLA2G4A-4 (Lnc-PLA2G4A-4-WT) and the design of Lnc-PLA2G4A-4 mutation sequence (Lnc-PLA2G4A-4-Mut). Down: luciferase reporter assays were performed in 293T cells co-transfected with the miR-23b-3p mimic and Lnc-PLA2G4A-4-WT or Lnc-PLA2G4A-4-Mut reporter vector. F. Relative expression of miR-23b in different HCC cell lines. G. Expression of miR-23b-3p in 50 normal tissue and 374 HCC tumor tissue from TCGA cohort in Student's unpaired t -test. H. Expression of miR-23b in 49 normal tissue and 49 HCC tumor tissue from TCGA cohort in Student's paired t -test. I. Relative expression of miR-23b in Lnc-PLA2G4A-4 over-expression cells or Lnc-PLA2G4A-4 knockdown cells, respectively. J. Correlation between miR-23b-3p and Lnc-PLA2G4A-4 expression in HCC tissues of MCHH. K. Correlation between miR-23b-3p and Lnc-PLA2G4A-4 expression in HCC tissues of TCGA.
    Figure Legend Snippet: Lnc-PLA2G4A-4 directly binds to miR-23b-3p. A. Fluorescence in Situ Hybridization assay used to examine the expression and location of Lnc-PLA2G4A-4 in SMMC-7721 and SK-Hep-1 cells. B. Cell fractionation assay used to examine the location of Lnc-PLA2G4A-4 in SMMC-7721 and SK-Hep-1 cells. C. The predicted results of Lnc-PLA2G4A-4 downstream target genes from three databases. D. Relative luciferase activities in 293T cells co-transfected with the mimic-NC/miR-567 mimic/miR-888 mimic/miR-23b-3p mimic and Lnc-PLA2G4A-4-WT reporter vector. E. Up: prediction of miR-23b-3p binding sites in Lnc-PLA2G4A-4 (Lnc-PLA2G4A-4-WT) and the design of Lnc-PLA2G4A-4 mutation sequence (Lnc-PLA2G4A-4-Mut). Down: luciferase reporter assays were performed in 293T cells co-transfected with the miR-23b-3p mimic and Lnc-PLA2G4A-4-WT or Lnc-PLA2G4A-4-Mut reporter vector. F. Relative expression of miR-23b in different HCC cell lines. G. Expression of miR-23b-3p in 50 normal tissue and 374 HCC tumor tissue from TCGA cohort in Student's unpaired t -test. H. Expression of miR-23b in 49 normal tissue and 49 HCC tumor tissue from TCGA cohort in Student's paired t -test. I. Relative expression of miR-23b in Lnc-PLA2G4A-4 over-expression cells or Lnc-PLA2G4A-4 knockdown cells, respectively. J. Correlation between miR-23b-3p and Lnc-PLA2G4A-4 expression in HCC tissues of MCHH. K. Correlation between miR-23b-3p and Lnc-PLA2G4A-4 expression in HCC tissues of TCGA.

    Techniques Used: Fluorescence, In Situ Hybridization, Expressing, Cell Fractionation, Luciferase, Transfection, Plasmid Preparation, Binding Assay, Mutagenesis, Sequencing, Over Expression

    human embryonic kidney cell line hek293t  (ATCC)


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    ATCC human embryonic kidney cell line hek293t
    A , B The expression of talin1 and talin2 were detected by western blot in cells of BCKDK overexpression or knockdown. C IF assay showed the colocalization of talin1 and BCKDK in MCF-7 cells. Cells were stained for BCKDK (red) and talin1 (green). Scale bar, 50 μm. D , E BCKDK was coimmunoprecipitated with talin1 in MCF-7 and MDA-MB-231 cells. F Exogenous Talin1 coimmunoprecipitated with BCKDK in <t>HEK293T</t> cells. G The ubiquitination of talin1 was examined by western blot in HEK293T cells.
    Human Embryonic Kidney Cell Line Hek293t, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "BCKDK regulates breast cancer cell adhesion and tumor metastasis by inhibiting TRIM21 ubiquitinate talin1"

    Article Title: BCKDK regulates breast cancer cell adhesion and tumor metastasis by inhibiting TRIM21 ubiquitinate talin1

    Journal: Cell Death & Disease

    doi: 10.1038/s41419-023-05944-4

    A , B The expression of talin1 and talin2 were detected by western blot in cells of BCKDK overexpression or knockdown. C IF assay showed the colocalization of talin1 and BCKDK in MCF-7 cells. Cells were stained for BCKDK (red) and talin1 (green). Scale bar, 50 μm. D , E BCKDK was coimmunoprecipitated with talin1 in MCF-7 and MDA-MB-231 cells. F Exogenous Talin1 coimmunoprecipitated with BCKDK in HEK293T cells. G The ubiquitination of talin1 was examined by western blot in HEK293T cells.
    Figure Legend Snippet: A , B The expression of talin1 and talin2 were detected by western blot in cells of BCKDK overexpression or knockdown. C IF assay showed the colocalization of talin1 and BCKDK in MCF-7 cells. Cells were stained for BCKDK (red) and talin1 (green). Scale bar, 50 μm. D , E BCKDK was coimmunoprecipitated with talin1 in MCF-7 and MDA-MB-231 cells. F Exogenous Talin1 coimmunoprecipitated with BCKDK in HEK293T cells. G The ubiquitination of talin1 was examined by western blot in HEK293T cells.

    Techniques Used: Expressing, Western Blot, Over Expression, Staining

    A The expression of talin1 was examined by western blot in HEK293T cells. B The expression of talin1 was examined by western blot in MDA-MB-231 cells. C Exogenous talin1 coimmunoprecipitated with TRIM21 in HEK293T cells. D The degradation protein level of talin1 detected in M231/Ctrl and M231/TRIM21 cells with CHX treatment (100 μg/mL) for indicated time intervals. E Co-IP shows that HA-ubiquitin is pulled down by talin1 in HEK293T cells. HEK293T cells were transfected with Myc-tagged talin1 and HA-ubiquitin, plus Flag-tagged TRIM21 or the vector controls. At 48 h post-transfection, cells were treated with MG132 for 4 h, and then lysates of these cells were subjected to IP with anti-Myc-conjugated beads. Immunoprecipitates were subjected to IB analysis for ubiquitinated talin1 with anti-ubiquitin or for indicated proteins. F HEK293T cells were transfected with Myc-tagged talin1 and HA-ubiquitin, plus Flag-tagged TRIM21, Flag-tagged BCKDK or their vector controls. At 48 h post-transfection, cells were lysed and subjected to IP with anti-Myc-conjugated beads. The immunoprecipitates were subjected to IB analysis for ubiquitinated talin1 with anti-ubiquitin or for indicated proteins. G IP analysis using anti-Myc antibody followed by IB analysis to detect HA-BCKDK and Flag-TRIM21 expression in HEK293T cells.
    Figure Legend Snippet: A The expression of talin1 was examined by western blot in HEK293T cells. B The expression of talin1 was examined by western blot in MDA-MB-231 cells. C Exogenous talin1 coimmunoprecipitated with TRIM21 in HEK293T cells. D The degradation protein level of talin1 detected in M231/Ctrl and M231/TRIM21 cells with CHX treatment (100 μg/mL) for indicated time intervals. E Co-IP shows that HA-ubiquitin is pulled down by talin1 in HEK293T cells. HEK293T cells were transfected with Myc-tagged talin1 and HA-ubiquitin, plus Flag-tagged TRIM21 or the vector controls. At 48 h post-transfection, cells were treated with MG132 for 4 h, and then lysates of these cells were subjected to IP with anti-Myc-conjugated beads. Immunoprecipitates were subjected to IB analysis for ubiquitinated talin1 with anti-ubiquitin or for indicated proteins. F HEK293T cells were transfected with Myc-tagged talin1 and HA-ubiquitin, plus Flag-tagged TRIM21, Flag-tagged BCKDK or their vector controls. At 48 h post-transfection, cells were lysed and subjected to IP with anti-Myc-conjugated beads. The immunoprecipitates were subjected to IB analysis for ubiquitinated talin1 with anti-ubiquitin or for indicated proteins. G IP analysis using anti-Myc antibody followed by IB analysis to detect HA-BCKDK and Flag-TRIM21 expression in HEK293T cells.

    Techniques Used: Expressing, Western Blot, Co-Immunoprecipitation Assay, Transfection, Plasmid Preparation

    human embryonic kidney hek 293t cell lines  (ATCC)


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    ATCC human embryonic kidney hek 293t cell lines
    Human Embryonic Kidney Hek 293t Cell Lines, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    human embryonic kidney cell line hek293t  (ATCC)


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    ATCC human embryonic kidney cell line hek293t
    (A) Western Blot analysis of expression levels of exogenous Flag-IL-17RA. 5 μg full-length Flag-IL-17RA plasmids were transiently transfected into <t>HEK293T</t> cells in a 10-cm dish. 18 hours (h) post transfection, cells were evenly split into 6-well plates. 42 h post transfection, the cells were treated with 20 μM MG132 or 0.5 μM MLN4924 for 8 h and 50 μg/ml CHX for indicated hours. Of note, in the group with CHX treatment for 8 h, MG132 or MLN4924 was added to all treatment groups simultaneously. Treatment of each subgroup was terminated at the same time, therefore CHX was added to another two subgroups 2 and 4 h before collecting cells. Overall, treatment time of MG132 and MLN4924 was 8 h and treatment time of CHX was 0, 2, 4, and 8 h, respectively. DMSO was used as control treatment. (B) Western blot analysis of endogenous IL-17RA in 22Rv1 cells after treatment with 20 μM MG132, 0.5 μM MLN4924 for 8h and 50 μg/ml CHX for indicated hours. DMSO was used as control treatment. (C) Western blot analysis of endogenous IL-17RA in HaCaT cell line after treatment with 10 μM of MG132 for 8 h and 50 μg/ml of CHX for indicated time. DMSO was used as control treatment. (D-F) Neddylation inhibitor MLN4924 at 0.1 μM, 0.5 μM, and 2.0 μM was used to treat HaCaT (D) , 22Rv1 (E) and PC-3 (F) cell lines for 6, 12 and 24 h. DMSO was used as control treatment. Each experiment was repeated at least 3 times.
    Human Embryonic Kidney Cell Line Hek293t, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "SCF FBXW11 complex targets interleukin-17 receptor A for ubiquitin-proteasome-mediated degradation"

    Article Title: SCF FBXW11 complex targets interleukin-17 receptor A for ubiquitin-proteasome-mediated degradation

    Journal: bioRxiv

    doi: 10.1101/2023.06.21.545972

    (A) Western Blot analysis of expression levels of exogenous Flag-IL-17RA. 5 μg full-length Flag-IL-17RA plasmids were transiently transfected into HEK293T cells in a 10-cm dish. 18 hours (h) post transfection, cells were evenly split into 6-well plates. 42 h post transfection, the cells were treated with 20 μM MG132 or 0.5 μM MLN4924 for 8 h and 50 μg/ml CHX for indicated hours. Of note, in the group with CHX treatment for 8 h, MG132 or MLN4924 was added to all treatment groups simultaneously. Treatment of each subgroup was terminated at the same time, therefore CHX was added to another two subgroups 2 and 4 h before collecting cells. Overall, treatment time of MG132 and MLN4924 was 8 h and treatment time of CHX was 0, 2, 4, and 8 h, respectively. DMSO was used as control treatment. (B) Western blot analysis of endogenous IL-17RA in 22Rv1 cells after treatment with 20 μM MG132, 0.5 μM MLN4924 for 8h and 50 μg/ml CHX for indicated hours. DMSO was used as control treatment. (C) Western blot analysis of endogenous IL-17RA in HaCaT cell line after treatment with 10 μM of MG132 for 8 h and 50 μg/ml of CHX for indicated time. DMSO was used as control treatment. (D-F) Neddylation inhibitor MLN4924 at 0.1 μM, 0.5 μM, and 2.0 μM was used to treat HaCaT (D) , 22Rv1 (E) and PC-3 (F) cell lines for 6, 12 and 24 h. DMSO was used as control treatment. Each experiment was repeated at least 3 times.
    Figure Legend Snippet: (A) Western Blot analysis of expression levels of exogenous Flag-IL-17RA. 5 μg full-length Flag-IL-17RA plasmids were transiently transfected into HEK293T cells in a 10-cm dish. 18 hours (h) post transfection, cells were evenly split into 6-well plates. 42 h post transfection, the cells were treated with 20 μM MG132 or 0.5 μM MLN4924 for 8 h and 50 μg/ml CHX for indicated hours. Of note, in the group with CHX treatment for 8 h, MG132 or MLN4924 was added to all treatment groups simultaneously. Treatment of each subgroup was terminated at the same time, therefore CHX was added to another two subgroups 2 and 4 h before collecting cells. Overall, treatment time of MG132 and MLN4924 was 8 h and treatment time of CHX was 0, 2, 4, and 8 h, respectively. DMSO was used as control treatment. (B) Western blot analysis of endogenous IL-17RA in 22Rv1 cells after treatment with 20 μM MG132, 0.5 μM MLN4924 for 8h and 50 μg/ml CHX for indicated hours. DMSO was used as control treatment. (C) Western blot analysis of endogenous IL-17RA in HaCaT cell line after treatment with 10 μM of MG132 for 8 h and 50 μg/ml of CHX for indicated time. DMSO was used as control treatment. (D-F) Neddylation inhibitor MLN4924 at 0.1 μM, 0.5 μM, and 2.0 μM was used to treat HaCaT (D) , 22Rv1 (E) and PC-3 (F) cell lines for 6, 12 and 24 h. DMSO was used as control treatment. Each experiment was repeated at least 3 times.

    Techniques Used: Western Blot, Expressing, Transfection

    (A) Phosphodegron TPxxE recognized by FBXW7 matches amino acid 780-785 of human IL-17RA. Phosphodegron DSGxxST recognized by FBXW1A/11 matches amino acid 725-732 of human IL-17RA. The phosphodegrons are conserved across different species. Diagram showing conserved domains, F-box domain and WD repeat domain, of FBXW family members. FBXW5 has a special D-box domain. (C) Percent identity of tryptophan-aspartic acid (WD) repeat domains of FBXW family members was computed with Clustal Omega algorithm . The plot was made using Prism GraphPad. (D) Binding of IL-17RA with FBXW7. HEK293T cells were seeded into 6-cm dishes at the density of 1 x 10^6. 1.5 µg full-length Flag-IL-17RA and 1.5 µg full-length HA-FBXW7 plasmids were transiently transfected using jetPRIME transfection reagent. An empty vector was used to compensate for the total amount of plasmids. 48 h post transfection, proteins were extracted using IP lysis buffer. The co-IP assays were carried out using 2 µg normal IgG (Cell signaling technology, #2729), 2 µg anti-Flag M2 or 12 µg anti-FBXW7. Experiments were repeated 4 times independently.
    Figure Legend Snippet: (A) Phosphodegron TPxxE recognized by FBXW7 matches amino acid 780-785 of human IL-17RA. Phosphodegron DSGxxST recognized by FBXW1A/11 matches amino acid 725-732 of human IL-17RA. The phosphodegrons are conserved across different species. Diagram showing conserved domains, F-box domain and WD repeat domain, of FBXW family members. FBXW5 has a special D-box domain. (C) Percent identity of tryptophan-aspartic acid (WD) repeat domains of FBXW family members was computed with Clustal Omega algorithm . The plot was made using Prism GraphPad. (D) Binding of IL-17RA with FBXW7. HEK293T cells were seeded into 6-cm dishes at the density of 1 x 10^6. 1.5 µg full-length Flag-IL-17RA and 1.5 µg full-length HA-FBXW7 plasmids were transiently transfected using jetPRIME transfection reagent. An empty vector was used to compensate for the total amount of plasmids. 48 h post transfection, proteins were extracted using IP lysis buffer. The co-IP assays were carried out using 2 µg normal IgG (Cell signaling technology, #2729), 2 µg anti-Flag M2 or 12 µg anti-FBXW7. Experiments were repeated 4 times independently.

    Techniques Used: Binding Assay, Transfection, Plasmid Preparation, Lysis, Co-Immunoprecipitation Assay

    (A) Binding of IL-17RA with E3 ligases. HEK293T cells were seeded at a density of 1 x 10^6 into 6-cm dishes. 20 h post-seeding, 1.5 µg full-length Flag-IL-17RA, 1.5 µg Myc-FBXW7 ΔF, 1.5 µg Myc-FBXW5, 1.5 µg Myc-FBXW1A and 1.5 µg Myc-Skp2 plasmids were transiently transfected using jetPRIME transfection reagent as indicated. An empty vector was used to compensate for the total amount of plasmids. 48 h post transfection, proteins were extracted using IP lysis buffer. The reciprocal co-IP assays were carried out using 1 µg anti-Flag M2 or 1 µg anti-c-Myc antibodies. Experiments were repeated 4 times independently. (B) Binding of IL-17RA with E3 ligases. HEK293T cells were seeded at a density of 1 x 10^6 into 6-cm dishes. 2 µg full-length Myc-His-IL-17RA, 2 µg Flag-FBXW2, 2 µg Flag-FBXW4, 1.5 µg Flag-HA-FBXW8, 1 µg Flag-HA-FBXW9, 2 µg Flag-HA-FBXW11, and 2 µg Flag-FBXW12 plasmids were transiently transfected using jetPRIME transfection reagent as indicated. An empty vector was used to compensate for the total amount of plasmids. 48 h post transfection, proteins were extracted using IP lysis buffer. The reciprocal co-IP assays were carried out using 1 µg anti-Flag M2 or 1 µg anti-c-Myc antibodies. Experiments were repeated 3 times independently. Asterisks indicate IgG heavy chain of antibodies used in co-IP. Experiments were repeated 4 times independently.
    Figure Legend Snippet: (A) Binding of IL-17RA with E3 ligases. HEK293T cells were seeded at a density of 1 x 10^6 into 6-cm dishes. 20 h post-seeding, 1.5 µg full-length Flag-IL-17RA, 1.5 µg Myc-FBXW7 ΔF, 1.5 µg Myc-FBXW5, 1.5 µg Myc-FBXW1A and 1.5 µg Myc-Skp2 plasmids were transiently transfected using jetPRIME transfection reagent as indicated. An empty vector was used to compensate for the total amount of plasmids. 48 h post transfection, proteins were extracted using IP lysis buffer. The reciprocal co-IP assays were carried out using 1 µg anti-Flag M2 or 1 µg anti-c-Myc antibodies. Experiments were repeated 4 times independently. (B) Binding of IL-17RA with E3 ligases. HEK293T cells were seeded at a density of 1 x 10^6 into 6-cm dishes. 2 µg full-length Myc-His-IL-17RA, 2 µg Flag-FBXW2, 2 µg Flag-FBXW4, 1.5 µg Flag-HA-FBXW8, 1 µg Flag-HA-FBXW9, 2 µg Flag-HA-FBXW11, and 2 µg Flag-FBXW12 plasmids were transiently transfected using jetPRIME transfection reagent as indicated. An empty vector was used to compensate for the total amount of plasmids. 48 h post transfection, proteins were extracted using IP lysis buffer. The reciprocal co-IP assays were carried out using 1 µg anti-Flag M2 or 1 µg anti-c-Myc antibodies. Experiments were repeated 3 times independently. Asterisks indicate IgG heavy chain of antibodies used in co-IP. Experiments were repeated 4 times independently.

    Techniques Used: Binding Assay, Transfection, Plasmid Preparation, Lysis, Co-Immunoprecipitation Assay

    (A) HEK293T cells were seeded into 10-cm dishes at a density of 4 x 10^6. 3 µg full-length Flag-IL-17RA, 2 µg HA-ubiquitin WT, 3 µg Flag-FBXW4, 3 µg Myc-FBXW5, 4 µg HA-FBXW7, 2 µg Flag-HA-FBXW9, 3 µg Flag-HA-FBXW11, and 3 µg Myc-FBXW1A plasmids were transiently transfected using jetPRIME transfection reagent as indicated. An empty vector was used to compensate for the total amount of plasmids. 42 h post transfection, transfected cells were treated with 10 µM MG132 for 6 h. Experiments were repeated 4 times independently. (B) THP-1 cells were seeded into 10-cm dishes at a density of 1.5 x 10^6. 24 h post seeding, 1 or 2 µg Flag-Ubv.Fw.11.2, 0.1 or 1 µg Flag-HA-FBXW11, and 2.5 µg His-ubiquitin WT plasmids were transfected using JetPrime transfection reagent. An empty vector was used to compensate for the total amount of plasmids. 42 h post transfection, 20 µM MG132 was added to treat the cells for 6 h. (C) HCT116 cells were seeded into 10-cm dishes at the density of 2 x 10^6. 24 h post seeding, 2 or 4 µg Flag-Ubv.Fw.11.2, 2 or 4 µg Flag-HA-FBXW11, and 2.5 µg His-ubiquitin WT plasmids were transfected using JetPrime transfection reagent. An empty vector was used to compensate for the total amount of plasmids. 42 h post transfection, 20 µM MG132 was added to treat the cells for 6 h. Experiments were repeated 4 times independently. (D) THP-1 cells were seeded into 10-cm dishes at a density of 1.5 x 10^6. 24 h post-seeding, 1 µg Flag-HA-FBXW11, and 2.5 µg WT or single lysine mutated His-ubiquitin plasmids were transfected using JetPrime transfection reagent. Empty vector was used to compensate for the total amount of plasmids in transfection. 42 h post-transfection, 20 µM MG132 was added to treat the cells for 6 h. Experiments were repeated 4 times independently. (E) HCT116 cells were seeded into 10-cm dishes at a density of 3 x 10^6. 24 h post-seeding, 2 or 4 µg Flag-HA-FBXW11, and 2.5 µg WT or single lysine mutated His-ubiquitin plasmids were transfected using JetPrime transfection reagent. Empty vector was used to compensate for the total amount of plasmids in transfection. 42 h post-transfection, 20 µM MG132 was added to treat the cells for 6 h. Experiments were repeated 3 times independently.
    Figure Legend Snippet: (A) HEK293T cells were seeded into 10-cm dishes at a density of 4 x 10^6. 3 µg full-length Flag-IL-17RA, 2 µg HA-ubiquitin WT, 3 µg Flag-FBXW4, 3 µg Myc-FBXW5, 4 µg HA-FBXW7, 2 µg Flag-HA-FBXW9, 3 µg Flag-HA-FBXW11, and 3 µg Myc-FBXW1A plasmids were transiently transfected using jetPRIME transfection reagent as indicated. An empty vector was used to compensate for the total amount of plasmids. 42 h post transfection, transfected cells were treated with 10 µM MG132 for 6 h. Experiments were repeated 4 times independently. (B) THP-1 cells were seeded into 10-cm dishes at a density of 1.5 x 10^6. 24 h post seeding, 1 or 2 µg Flag-Ubv.Fw.11.2, 0.1 or 1 µg Flag-HA-FBXW11, and 2.5 µg His-ubiquitin WT plasmids were transfected using JetPrime transfection reagent. An empty vector was used to compensate for the total amount of plasmids. 42 h post transfection, 20 µM MG132 was added to treat the cells for 6 h. (C) HCT116 cells were seeded into 10-cm dishes at the density of 2 x 10^6. 24 h post seeding, 2 or 4 µg Flag-Ubv.Fw.11.2, 2 or 4 µg Flag-HA-FBXW11, and 2.5 µg His-ubiquitin WT plasmids were transfected using JetPrime transfection reagent. An empty vector was used to compensate for the total amount of plasmids. 42 h post transfection, 20 µM MG132 was added to treat the cells for 6 h. Experiments were repeated 4 times independently. (D) THP-1 cells were seeded into 10-cm dishes at a density of 1.5 x 10^6. 24 h post-seeding, 1 µg Flag-HA-FBXW11, and 2.5 µg WT or single lysine mutated His-ubiquitin plasmids were transfected using JetPrime transfection reagent. Empty vector was used to compensate for the total amount of plasmids in transfection. 42 h post-transfection, 20 µM MG132 was added to treat the cells for 6 h. Experiments were repeated 4 times independently. (E) HCT116 cells were seeded into 10-cm dishes at a density of 3 x 10^6. 24 h post-seeding, 2 or 4 µg Flag-HA-FBXW11, and 2.5 µg WT or single lysine mutated His-ubiquitin plasmids were transfected using JetPrime transfection reagent. Empty vector was used to compensate for the total amount of plasmids in transfection. 42 h post-transfection, 20 µM MG132 was added to treat the cells for 6 h. Experiments were repeated 3 times independently.

    Techniques Used: Transfection, Plasmid Preparation

    (A) 21 h before transfection, HEK293T cells were seeded into 10-cm dishes at a density of 4.5 x 10^6. 1.5 µg full-length Flag-IL17RA, 3 µg His-ubiquitin WT, 2 µg Myc-FBXW5, 1.5 µg Flag-HA-FBXW9, 3.5 µg Flag-HA-FBXW11, 3.5 µg Myc-FBXW1A, and various amounts of empty vector (to compensate for the total amount of plasmids) were transiently transfected using jetPRIME transfection reagent as indicated; 40 h post transfection, 20 µM MG132 was added to treat cells for 8 h.
    Figure Legend Snippet: (A) 21 h before transfection, HEK293T cells were seeded into 10-cm dishes at a density of 4.5 x 10^6. 1.5 µg full-length Flag-IL17RA, 3 µg His-ubiquitin WT, 2 µg Myc-FBXW5, 1.5 µg Flag-HA-FBXW9, 3.5 µg Flag-HA-FBXW11, 3.5 µg Myc-FBXW1A, and various amounts of empty vector (to compensate for the total amount of plasmids) were transiently transfected using jetPRIME transfection reagent as indicated; 40 h post transfection, 20 µM MG132 was added to treat cells for 8 h.

    Techniques Used: Transfection, Plasmid Preparation

    (A) Total RNA was isolated from 12 cell lines, including HEK293T, HaCaT, A-431, Ishikawa, HeLa, A549, THP-1, HCT116, DLD1, 22RV1, PC-3, and LNCaP. Real-time qPCR analysis was conducted to measure FBXW11 mRNA levels. HEK293T cell line was used as calibration control and Student’s t test was used to determine statistical significance when compared to HEK293T. ** P< 0.01, *** P< 0.001, and **** P< 0.0001. Data were collected from 3 independent biological replicates. (B) Western blot analysis was used to determine IL-17RA protein levels across 12 cell lines, including HEK293T, HaCaT, A-431, Ishikawa, HeLa, A549, THP-1, HCT116, DLD1, 22RV1, PC-3, and LNCaP. “Long” indicates long exposure and “Short” indicates short exposure. Signal intensities of IL-17RA and Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) in each cell line were determined using Image Studio (Lite Ver 5.2, Li-Cor) software. The ratio of IL-17RA/GAPDH was then calculated to compare relative protein levels. HEK293T cell line was used as calibration control. Data were collected from 3 independent replicates. (C) The quantification results shown in (A) and (B) were plotted to illustrate the trajectory of relative FBXW11 mRNA levels and IL-17RA protein levels across the 12 human cell lines. Error bar represents mean ± standard deviation (S.D.). (D) Pearson’s correlation analysis was conducted using the data of relative FBXW11 mRNA levels and relative IL-17RA protein levels. (E) Proteomic data obtained from CPTAC database demonstrated IL-17RA and FBXW11 protein levels among glioblastoma multiform (brain tumors), uterus corpus endometrial cancer (UCEC, uterine tumors) and corresponding normal control tissues. Z-value indicates standard deviations from the median across samples for the given cancer type. The Student’s t test was used to determine statistical significance between normal control tissues and tumors. *** P < 0.001 and **** P <0.0001. (F) Pearson’s correlation analysis was conducted using the proteomic data on FBXW11 and IL-17RA protein levels of glioblastoma multiform and normal control tissues. (G) Pearson’s correlation analysis was conducted using the proteomic data on FBXW11 and IL-17RA protein levels of UCEC and normal control tissues. Control tissues of glioblastoma were from the frontal cortex. Control tissues of uterine tumors were from endometrium (with or without enrichment) and myometrium.
    Figure Legend Snippet: (A) Total RNA was isolated from 12 cell lines, including HEK293T, HaCaT, A-431, Ishikawa, HeLa, A549, THP-1, HCT116, DLD1, 22RV1, PC-3, and LNCaP. Real-time qPCR analysis was conducted to measure FBXW11 mRNA levels. HEK293T cell line was used as calibration control and Student’s t test was used to determine statistical significance when compared to HEK293T. ** P< 0.01, *** P< 0.001, and **** P< 0.0001. Data were collected from 3 independent biological replicates. (B) Western blot analysis was used to determine IL-17RA protein levels across 12 cell lines, including HEK293T, HaCaT, A-431, Ishikawa, HeLa, A549, THP-1, HCT116, DLD1, 22RV1, PC-3, and LNCaP. “Long” indicates long exposure and “Short” indicates short exposure. Signal intensities of IL-17RA and Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) in each cell line were determined using Image Studio (Lite Ver 5.2, Li-Cor) software. The ratio of IL-17RA/GAPDH was then calculated to compare relative protein levels. HEK293T cell line was used as calibration control. Data were collected from 3 independent replicates. (C) The quantification results shown in (A) and (B) were plotted to illustrate the trajectory of relative FBXW11 mRNA levels and IL-17RA protein levels across the 12 human cell lines. Error bar represents mean ± standard deviation (S.D.). (D) Pearson’s correlation analysis was conducted using the data of relative FBXW11 mRNA levels and relative IL-17RA protein levels. (E) Proteomic data obtained from CPTAC database demonstrated IL-17RA and FBXW11 protein levels among glioblastoma multiform (brain tumors), uterus corpus endometrial cancer (UCEC, uterine tumors) and corresponding normal control tissues. Z-value indicates standard deviations from the median across samples for the given cancer type. The Student’s t test was used to determine statistical significance between normal control tissues and tumors. *** P < 0.001 and **** P <0.0001. (F) Pearson’s correlation analysis was conducted using the proteomic data on FBXW11 and IL-17RA protein levels of glioblastoma multiform and normal control tissues. (G) Pearson’s correlation analysis was conducted using the proteomic data on FBXW11 and IL-17RA protein levels of UCEC and normal control tissues. Control tissues of glioblastoma were from the frontal cortex. Control tissues of uterine tumors were from endometrium (with or without enrichment) and myometrium.

    Techniques Used: Isolation, Western Blot, Software, Standard Deviation

    (A) Schematic diagram of full-length IL-17RA (Flag-IL-17RA FL) and truncated mutants (Flag-IL-17RA Δ729-773 and Flag-IL-17RA Δ665-804) used in this study. (B) Binding of full-length IL-17RA and truncated mutants with FBXW1A and FBXW11. HEK293T cells were seeded into 10-cm dishes at a density of 2.0 x 10^6. 20 h post-seeding, 1.5 μg Flag-IL-17RA FL, 1.5 μg Flag-IL-17RA Δ729-773, 1 μg Flag-IL-17RA Δ665-804, 1.5 μg Myc-FBXW1A, and 1.5 μg Flag-HA-Fbxw11 were transiently transfected using jetPRIME transfection reagent as indicated. Empty vector was used to compensate for the total amount of plasmids in transfection. 48 h post transfection, the whole cell lysates were extracted for subsequent co-IP and Western blot analyses. (C) Ubiquitylation of Flag-IL-17RA Δ665-804 by FBXW11 was less than Flag-IL-17RA FL. HEK293T cells were seeded into 10-cm dishes at a density of 4.5 x 10^6. 24 h post-seeding, 1 µg Flag-IL-17RA full-length, 0.75 µg Flag-IL-17RA Δ665-804, 3.5 µg Flag-HA-FBXW11, 2.5 µg His-ubiquitin WT plasmids were transfected using jetPRIME transfection reagent as indicated. 40 h post-transfection, the cells were treated with 20 µM MG132 for 8 h. Precipitates pulled-down by Ni-NTA resins and corresponding whole cell lysate (WCL) were subject to Western blot analysis. (D) Western Blot analysis of protein stability of Flag-IL-17RA FL and Flag-IL-17RA Δ665-804. 1.5 µg Flag-IL-17RA FL or 1.5 µg Flag-IL-17RA Δ665-804 plasmids were transiently transfected into 1.5 x 10^6 HEK293T cells in a 6-cm dish. 24 h post-transfection, the cells were treated with 10 μM MG132 for 24 h and 50 μg/ml CHX for indicated time. DMSO was applied as control treatment. Experiments were repeated 4 times independently. (E) Quantification of ratio of exogenous Flag-IL-17RA FL/GAPDH after treatment with MG132 and CHX. The t 1/2 means half-life of IL-17RA FL. Statistical significance was conducted using a two-way ANOVA with Šídák’s multiple comparison test. Error bar represents mean ± standard deviation (S.D.). * P < 0.05. (F) Quantification of ratio of exogenous Flag-IL-17RA Δ665-804 to GAPDH after treatment with MG132 and CHX. The t 1/2 means half-life of IL-17RA Δ665-804. Statistical significance was computed using a two-way ANOVA with Šídák’s multiple comparison test. Error bar represents mean ± standard deviation (S.D.). The “ns” means no statistical significance. Experiments were repeated 3 times independently.
    Figure Legend Snippet: (A) Schematic diagram of full-length IL-17RA (Flag-IL-17RA FL) and truncated mutants (Flag-IL-17RA Δ729-773 and Flag-IL-17RA Δ665-804) used in this study. (B) Binding of full-length IL-17RA and truncated mutants with FBXW1A and FBXW11. HEK293T cells were seeded into 10-cm dishes at a density of 2.0 x 10^6. 20 h post-seeding, 1.5 μg Flag-IL-17RA FL, 1.5 μg Flag-IL-17RA Δ729-773, 1 μg Flag-IL-17RA Δ665-804, 1.5 μg Myc-FBXW1A, and 1.5 μg Flag-HA-Fbxw11 were transiently transfected using jetPRIME transfection reagent as indicated. Empty vector was used to compensate for the total amount of plasmids in transfection. 48 h post transfection, the whole cell lysates were extracted for subsequent co-IP and Western blot analyses. (C) Ubiquitylation of Flag-IL-17RA Δ665-804 by FBXW11 was less than Flag-IL-17RA FL. HEK293T cells were seeded into 10-cm dishes at a density of 4.5 x 10^6. 24 h post-seeding, 1 µg Flag-IL-17RA full-length, 0.75 µg Flag-IL-17RA Δ665-804, 3.5 µg Flag-HA-FBXW11, 2.5 µg His-ubiquitin WT plasmids were transfected using jetPRIME transfection reagent as indicated. 40 h post-transfection, the cells were treated with 20 µM MG132 for 8 h. Precipitates pulled-down by Ni-NTA resins and corresponding whole cell lysate (WCL) were subject to Western blot analysis. (D) Western Blot analysis of protein stability of Flag-IL-17RA FL and Flag-IL-17RA Δ665-804. 1.5 µg Flag-IL-17RA FL or 1.5 µg Flag-IL-17RA Δ665-804 plasmids were transiently transfected into 1.5 x 10^6 HEK293T cells in a 6-cm dish. 24 h post-transfection, the cells were treated with 10 μM MG132 for 24 h and 50 μg/ml CHX for indicated time. DMSO was applied as control treatment. Experiments were repeated 4 times independently. (E) Quantification of ratio of exogenous Flag-IL-17RA FL/GAPDH after treatment with MG132 and CHX. The t 1/2 means half-life of IL-17RA FL. Statistical significance was conducted using a two-way ANOVA with Šídák’s multiple comparison test. Error bar represents mean ± standard deviation (S.D.). * P < 0.05. (F) Quantification of ratio of exogenous Flag-IL-17RA Δ665-804 to GAPDH after treatment with MG132 and CHX. The t 1/2 means half-life of IL-17RA Δ665-804. Statistical significance was computed using a two-way ANOVA with Šídák’s multiple comparison test. Error bar represents mean ± standard deviation (S.D.). The “ns” means no statistical significance. Experiments were repeated 3 times independently.

    Techniques Used: Binding Assay, Transfection, Plasmid Preparation, Co-Immunoprecipitation Assay, Western Blot, Standard Deviation

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    See also Extended Data Fig. 4. (a) Heatmap of miRNA expression in A549-Ctrl and A549-N cells based on small RNA sequencing. (b) Quantification of five miRNAs in A549-Ctrl and A549-N cells. (c) Ratio of cytosolic pre-miRNA levels to nuclear pre-miRNA levels in A549-Ctrl and A549-N cells. (d) Ratio of cytosolic pre-miRNA levels to nuclear pre-miRNA levels in A549-Ctrl and A549-N cells transfected with a plasmid expressing XPO5 or control plasmid. (e) Ratio of mature miRNA levels to pre-miRNA levels in A549-Ctrl and A549-N cells. (f) Ratio of mature miRNA levels to pre-miRNA levels in A549-Ctrl and A549-N cells transfected with a plasmid expressing Dicer or control plasmid. (g) miRNA levels in A549-Ctrl or A549-N cells co-transfected with XPO5-expressing and Dicer-expressing plasmids. (h) Luciferase assay of HEK293T cells following co-transfection of splicing reporter with SRSF3-specific siRNA (siSRSF3), hnRNPA3-specific siRNA (sihnRNPA3), or control siRNA. (i) Luciferase assay of HEK293T-Ctrl or HEK293T-N cells following co-transfection of splicing reporter with SRSF3-expressing, hnRNPA3-expressing, or control plasmids. (j) Changes in percent spliced-in (PSI) values between A549-Ctrl and A549-N cells determined using full-length transcriptome sequencing data. ΔPSI = PSI(A549-N) − PSI(A549-Ctrl). (k) Relative fraction of transcripts with intron retention over total sequencing reads determined using full-length transcriptome sequencing data. (l) Relative intronic and exonic RNA levels of the indicated genes in A549-Ctrl and A549-N cells. (m) Relative intronic and exonic RNA levels of the indicated genes in A549-Ctrl and A549-N cells co-transfected with SRSF3-expressing and hnRNPA3-expressing plasmids. Data in b–i and k–m are expressed as mean ± SD of three biological replicates. **p < 0.01; *p < 0.05; ns, not significant (p > 0.05; two-sided Student’s t -test). Ctrl: control plasmid; N: N protein; siNC: negative control siRNA; SES: single exon skipping; MES: multiple exon skipping; MXE: mutually exclusive exons; A5SS or A3SS: alternative 5′ and 3′ splice sites, respectively; IR: intron retention.

    Journal: bioRxiv

    Article Title: SARS-CoV-2 N protein-induced Dicer, XPO5, SRSF3, and hnRNPA3 downregulation causes pneumonia

    doi: 10.1101/2023.10.03.560426

    Figure Lengend Snippet: See also Extended Data Fig. 4. (a) Heatmap of miRNA expression in A549-Ctrl and A549-N cells based on small RNA sequencing. (b) Quantification of five miRNAs in A549-Ctrl and A549-N cells. (c) Ratio of cytosolic pre-miRNA levels to nuclear pre-miRNA levels in A549-Ctrl and A549-N cells. (d) Ratio of cytosolic pre-miRNA levels to nuclear pre-miRNA levels in A549-Ctrl and A549-N cells transfected with a plasmid expressing XPO5 or control plasmid. (e) Ratio of mature miRNA levels to pre-miRNA levels in A549-Ctrl and A549-N cells. (f) Ratio of mature miRNA levels to pre-miRNA levels in A549-Ctrl and A549-N cells transfected with a plasmid expressing Dicer or control plasmid. (g) miRNA levels in A549-Ctrl or A549-N cells co-transfected with XPO5-expressing and Dicer-expressing plasmids. (h) Luciferase assay of HEK293T cells following co-transfection of splicing reporter with SRSF3-specific siRNA (siSRSF3), hnRNPA3-specific siRNA (sihnRNPA3), or control siRNA. (i) Luciferase assay of HEK293T-Ctrl or HEK293T-N cells following co-transfection of splicing reporter with SRSF3-expressing, hnRNPA3-expressing, or control plasmids. (j) Changes in percent spliced-in (PSI) values between A549-Ctrl and A549-N cells determined using full-length transcriptome sequencing data. ΔPSI = PSI(A549-N) − PSI(A549-Ctrl). (k) Relative fraction of transcripts with intron retention over total sequencing reads determined using full-length transcriptome sequencing data. (l) Relative intronic and exonic RNA levels of the indicated genes in A549-Ctrl and A549-N cells. (m) Relative intronic and exonic RNA levels of the indicated genes in A549-Ctrl and A549-N cells co-transfected with SRSF3-expressing and hnRNPA3-expressing plasmids. Data in b–i and k–m are expressed as mean ± SD of three biological replicates. **p < 0.01; *p < 0.05; ns, not significant (p > 0.05; two-sided Student’s t -test). Ctrl: control plasmid; N: N protein; siNC: negative control siRNA; SES: single exon skipping; MES: multiple exon skipping; MXE: mutually exclusive exons; A5SS or A3SS: alternative 5′ and 3′ splice sites, respectively; IR: intron retention.

    Article Snippet: The human lung adenocarcinoma epithelial cell line A549 (male, CCL-185), human bronchial epithelial cell line BEAS-2B (male, CRL-9609), and human embryonic kidney cell line HEK293T (female, CRL-3216) were obtained from the American Type Culture Collection (Manassas, VA, USA).

    Techniques: Expressing, RNA Sequencing Assay, Transfection, Plasmid Preparation, Luciferase, Cotransfection, Sequencing, Negative Control

    Lnc-PLA2G4A-4 directly binds to miR-23b-3p. A. Fluorescence in Situ Hybridization assay used to examine the expression and location of Lnc-PLA2G4A-4 in SMMC-7721 and SK-Hep-1 cells. B. Cell fractionation assay used to examine the location of Lnc-PLA2G4A-4 in SMMC-7721 and SK-Hep-1 cells. C. The predicted results of Lnc-PLA2G4A-4 downstream target genes from three databases. D. Relative luciferase activities in 293T cells co-transfected with the mimic-NC/miR-567 mimic/miR-888 mimic/miR-23b-3p mimic and Lnc-PLA2G4A-4-WT reporter vector. E. Up: prediction of miR-23b-3p binding sites in Lnc-PLA2G4A-4 (Lnc-PLA2G4A-4-WT) and the design of Lnc-PLA2G4A-4 mutation sequence (Lnc-PLA2G4A-4-Mut). Down: luciferase reporter assays were performed in 293T cells co-transfected with the miR-23b-3p mimic and Lnc-PLA2G4A-4-WT or Lnc-PLA2G4A-4-Mut reporter vector. F. Relative expression of miR-23b in different HCC cell lines. G. Expression of miR-23b-3p in 50 normal tissue and 374 HCC tumor tissue from TCGA cohort in Student's unpaired t -test. H. Expression of miR-23b in 49 normal tissue and 49 HCC tumor tissue from TCGA cohort in Student's paired t -test. I. Relative expression of miR-23b in Lnc-PLA2G4A-4 over-expression cells or Lnc-PLA2G4A-4 knockdown cells, respectively. J. Correlation between miR-23b-3p and Lnc-PLA2G4A-4 expression in HCC tissues of MCHH. K. Correlation between miR-23b-3p and Lnc-PLA2G4A-4 expression in HCC tissues of TCGA.

    Journal: Heliyon

    Article Title: Lnc-PLA2G4A-4 facilitates the progression of hepatocellular carcinoma by inducing versican expression via sponging miR-23b-3p

    doi: 10.1016/j.heliyon.2023.e18698

    Figure Lengend Snippet: Lnc-PLA2G4A-4 directly binds to miR-23b-3p. A. Fluorescence in Situ Hybridization assay used to examine the expression and location of Lnc-PLA2G4A-4 in SMMC-7721 and SK-Hep-1 cells. B. Cell fractionation assay used to examine the location of Lnc-PLA2G4A-4 in SMMC-7721 and SK-Hep-1 cells. C. The predicted results of Lnc-PLA2G4A-4 downstream target genes from three databases. D. Relative luciferase activities in 293T cells co-transfected with the mimic-NC/miR-567 mimic/miR-888 mimic/miR-23b-3p mimic and Lnc-PLA2G4A-4-WT reporter vector. E. Up: prediction of miR-23b-3p binding sites in Lnc-PLA2G4A-4 (Lnc-PLA2G4A-4-WT) and the design of Lnc-PLA2G4A-4 mutation sequence (Lnc-PLA2G4A-4-Mut). Down: luciferase reporter assays were performed in 293T cells co-transfected with the miR-23b-3p mimic and Lnc-PLA2G4A-4-WT or Lnc-PLA2G4A-4-Mut reporter vector. F. Relative expression of miR-23b in different HCC cell lines. G. Expression of miR-23b-3p in 50 normal tissue and 374 HCC tumor tissue from TCGA cohort in Student's unpaired t -test. H. Expression of miR-23b in 49 normal tissue and 49 HCC tumor tissue from TCGA cohort in Student's paired t -test. I. Relative expression of miR-23b in Lnc-PLA2G4A-4 over-expression cells or Lnc-PLA2G4A-4 knockdown cells, respectively. J. Correlation between miR-23b-3p and Lnc-PLA2G4A-4 expression in HCC tissues of MCHH. K. Correlation between miR-23b-3p and Lnc-PLA2G4A-4 expression in HCC tissues of TCGA.

    Article Snippet: Human HCC cell line SNU398, SNU449, SK-Hep-1, Hep3B, HepG2/C3A, as well as Human Embryonic Kidney 293T (HEK-293T) cell line were purchased from the American Type Culture Collection (ATCC, USA).

    Techniques: Fluorescence, In Situ Hybridization, Expressing, Cell Fractionation, Luciferase, Transfection, Plasmid Preparation, Binding Assay, Mutagenesis, Sequencing, Over Expression