kaiso  (Agilent technologies)


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    Agilent technologies kaiso
    Kaiso, supplied by Agilent technologies, 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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    kaiso - by Bioz Stars, 2024-09
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    kaiso protein  (Active Motif)

     
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    Active Motif kaiso protein
    KBSs in human and mouse H19 ICR. A Human Igf2/H19 locus structure. The enlarged map shows the region of the human H19 ICR (IC1) that we previously used as a transgene. Human IC1 has repetitive structures (A-repeats 1 and 2, and B-repeats 1–7) , with a KBS (indicated as a star) located within the B4 repeat. Dots (0–7) and black boxes indicate CTCF binding sites [ , ] and Sox-Oct motifs [ , ], respectively. B Mouse Igf2/H19 locus structure. The enlarged map shows the region of the mouse H19 ICR that we previously used as a transgene. Dots (1–4) indicate CTCF-binding sites [ , ]. The black box indicates the 'b' region containing Sox-Oct motifs . The nucleotide sequence of the 118-bp region is shown below the map. RCTG motifs I–V are shown in black and white inverted. Gray boxes indicate 5ʹ- and 3ʹ-KBSs. Mutated nucleotides in Δ5- H19 ICR and the region deleted from Δ36- H19 ICR mutants are indicated below the sequence . C Nucleotide sequences of the KBSs in the human IC1 B4 repeat and in the mouse H19 ICR 118-bp region. Double-stranded DNA fragments with these sequences were used either as a probe or as competitors in ( D ). D EMSA performed on nuclear extract <t>from</t> <t>HEK293T</t> cells overexpressing FLAG-tagged <t>Kaiso</t> protein and the B4-KBS probe. Three micrograms of nuclear extract were used in lane 3 and 7 μg in the others. Two hundred- and 800-times molar excess of competitors were used
    Kaiso Protein, supplied by Active Motif, 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/kaiso protein/product/Active Motif
    Average 86 stars, based on 1 article reviews
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    kaiso protein - by Bioz Stars, 2024-09
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    1) Product Images from "Imprinted DNA methylation of the H19 ICR is established and maintained in vivo in the absence of Kaiso"

    Article Title: Imprinted DNA methylation of the H19 ICR is established and maintained in vivo in the absence of Kaiso

    Journal: Epigenetics & Chromatin

    doi: 10.1186/s13072-024-00544-8

    KBSs in human and mouse H19 ICR. A Human Igf2/H19 locus structure. The enlarged map shows the region of the human H19 ICR (IC1) that we previously used as a transgene. Human IC1 has repetitive structures (A-repeats 1 and 2, and B-repeats 1–7) , with a KBS (indicated as a star) located within the B4 repeat. Dots (0–7) and black boxes indicate CTCF binding sites [ , ] and Sox-Oct motifs [ , ], respectively. B Mouse Igf2/H19 locus structure. The enlarged map shows the region of the mouse H19 ICR that we previously used as a transgene. Dots (1–4) indicate CTCF-binding sites [ , ]. The black box indicates the 'b' region containing Sox-Oct motifs . The nucleotide sequence of the 118-bp region is shown below the map. RCTG motifs I–V are shown in black and white inverted. Gray boxes indicate 5ʹ- and 3ʹ-KBSs. Mutated nucleotides in Δ5- H19 ICR and the region deleted from Δ36- H19 ICR mutants are indicated below the sequence . C Nucleotide sequences of the KBSs in the human IC1 B4 repeat and in the mouse H19 ICR 118-bp region. Double-stranded DNA fragments with these sequences were used either as a probe or as competitors in ( D ). D EMSA performed on nuclear extract from HEK293T cells overexpressing FLAG-tagged Kaiso protein and the B4-KBS probe. Three micrograms of nuclear extract were used in lane 3 and 7 μg in the others. Two hundred- and 800-times molar excess of competitors were used
    Figure Legend Snippet: KBSs in human and mouse H19 ICR. A Human Igf2/H19 locus structure. The enlarged map shows the region of the human H19 ICR (IC1) that we previously used as a transgene. Human IC1 has repetitive structures (A-repeats 1 and 2, and B-repeats 1–7) , with a KBS (indicated as a star) located within the B4 repeat. Dots (0–7) and black boxes indicate CTCF binding sites [ , ] and Sox-Oct motifs [ , ], respectively. B Mouse Igf2/H19 locus structure. The enlarged map shows the region of the mouse H19 ICR that we previously used as a transgene. Dots (1–4) indicate CTCF-binding sites [ , ]. The black box indicates the 'b' region containing Sox-Oct motifs . The nucleotide sequence of the 118-bp region is shown below the map. RCTG motifs I–V are shown in black and white inverted. Gray boxes indicate 5ʹ- and 3ʹ-KBSs. Mutated nucleotides in Δ5- H19 ICR and the region deleted from Δ36- H19 ICR mutants are indicated below the sequence . C Nucleotide sequences of the KBSs in the human IC1 B4 repeat and in the mouse H19 ICR 118-bp region. Double-stranded DNA fragments with these sequences were used either as a probe or as competitors in ( D ). D EMSA performed on nuclear extract from HEK293T cells overexpressing FLAG-tagged Kaiso protein and the B4-KBS probe. Three micrograms of nuclear extract were used in lane 3 and 7 μg in the others. Two hundred- and 800-times molar excess of competitors were used

    Techniques Used: Binding Assay, Sequencing

    kaiso zbtb33 rabbit polyclonal antibody  (ABclonal Biotechnology)

     
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    ABclonal Biotechnology kaiso zbtb33 rabbit polyclonal antibody
    Kaiso Zbtb33 Rabbit Polyclonal Antibody, supplied by ABclonal Biotechnology, 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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    sirna ‑ zbtb33 kaiso knockdown  (Revvity Signals)

     
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    Revvity Signals sirna ‑ zbtb33 kaiso knockdown
    Sirna ‑ Zbtb33 Kaiso Knockdown, supplied by Revvity Signals, 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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    rest sirna kaiso sirna  (Revvity Signals)

     
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    Revvity Signals rest sirna kaiso sirna
    Rest Sirna Kaiso Sirna, supplied by Revvity Signals, 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/rest sirna kaiso sirna/product/Revvity Signals
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    rest sirna kaiso sirna  (Revvity Signals)

     
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    Revvity Signals rest sirna kaiso sirna
    Effects of <t>REST</t> knockdown on gene expression in IDH-WT and IDH-MUT U87 cells. A Sorted values of log2 fold change (log2 FC) for DEGs in the IDH-MUT vs IDH-WT comparison in U87 cells are presented as red dots. Values for the same genes inferred from the IDH-MUT vs IDH-WT comparison in TCGA G2/G3 gliomas are overlaid as gray dots. Percentage of log2 FC direction concordance between IDH-MUT vs IDH-WT in U87 cells and glioma tumors was calculated. A number of DEGs is indicated. Black vertical line separates genes with higher expression in IDH-MUT U87 versus IDH-WT U87 from the genes with higher expression in IDH-WT U87 versus IDH-MUT U87. B Relative expression of REST in IDH-WT and IDH-MUT U87 cells at 72 h of REST silencing with <t>siRNA.</t> mRNA levels in transfected cells were determined with quantitative PCR and normalized to GAPDH expression in the same sample. Data are represented as mean ± SEM, n = 4 independent experiments, * p < 0.05, two-tailed Mann–Whitney test (WT: p = 0.0286; MUT: p = 0.0286). C Levels of REST protein in IDH-WT and IDH-MUT U87 cells at 72 h after transfection with control or REST specific siRNAs determined with Western blotting. Immunoblots were analyzed by densitometry. Data are represented as mean ± SEM, n = 4. ** p < 0.01 (WT: p = 0.0018, MUT: p = 0.0052; two-tailed ratio-paired t -test). No difference was observed in the level of REST protein between IDH-MUT and IDH-WT controls (siCTRL) ( p = 0.226). D Volcano plots of the genes differentially expressed between siCTRL and siREST-transfected IDH-WT (upper plot) or IDH-MUT (bottom plot) U87 glioma cells. The axes show log2 fold change (x-axis) and -log10 from adjusted q-value (y-axis). E Gene Ontology (GO) Biological Processes (BP) analysis was performed on DEGs common in IDH-WT and IDH-MUT U87 cells. The results are presented as bar plots for pathways upregulated (upper panel) and downregulated (bottom panel) in REST depleted cells
    Rest Sirna Kaiso Sirna, supplied by Revvity Signals, 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/rest sirna kaiso sirna/product/Revvity Signals
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    rest sirna kaiso sirna - by Bioz Stars, 2024-09
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    1) Product Images from "Comprehensive analysis of the REST transcription factor regulatory networks in IDH mutant and IDH wild-type glioma cell lines and tumors"

    Article Title: Comprehensive analysis of the REST transcription factor regulatory networks in IDH mutant and IDH wild-type glioma cell lines and tumors

    Journal: Acta Neuropathologica Communications

    doi: 10.1186/s40478-024-01779-y

    Effects of REST knockdown on gene expression in IDH-WT and IDH-MUT U87 cells. A Sorted values of log2 fold change (log2 FC) for DEGs in the IDH-MUT vs IDH-WT comparison in U87 cells are presented as red dots. Values for the same genes inferred from the IDH-MUT vs IDH-WT comparison in TCGA G2/G3 gliomas are overlaid as gray dots. Percentage of log2 FC direction concordance between IDH-MUT vs IDH-WT in U87 cells and glioma tumors was calculated. A number of DEGs is indicated. Black vertical line separates genes with higher expression in IDH-MUT U87 versus IDH-WT U87 from the genes with higher expression in IDH-WT U87 versus IDH-MUT U87. B Relative expression of REST in IDH-WT and IDH-MUT U87 cells at 72 h of REST silencing with siRNA. mRNA levels in transfected cells were determined with quantitative PCR and normalized to GAPDH expression in the same sample. Data are represented as mean ± SEM, n = 4 independent experiments, * p < 0.05, two-tailed Mann–Whitney test (WT: p = 0.0286; MUT: p = 0.0286). C Levels of REST protein in IDH-WT and IDH-MUT U87 cells at 72 h after transfection with control or REST specific siRNAs determined with Western blotting. Immunoblots were analyzed by densitometry. Data are represented as mean ± SEM, n = 4. ** p < 0.01 (WT: p = 0.0018, MUT: p = 0.0052; two-tailed ratio-paired t -test). No difference was observed in the level of REST protein between IDH-MUT and IDH-WT controls (siCTRL) ( p = 0.226). D Volcano plots of the genes differentially expressed between siCTRL and siREST-transfected IDH-WT (upper plot) or IDH-MUT (bottom plot) U87 glioma cells. The axes show log2 fold change (x-axis) and -log10 from adjusted q-value (y-axis). E Gene Ontology (GO) Biological Processes (BP) analysis was performed on DEGs common in IDH-WT and IDH-MUT U87 cells. The results are presented as bar plots for pathways upregulated (upper panel) and downregulated (bottom panel) in REST depleted cells
    Figure Legend Snippet: Effects of REST knockdown on gene expression in IDH-WT and IDH-MUT U87 cells. A Sorted values of log2 fold change (log2 FC) for DEGs in the IDH-MUT vs IDH-WT comparison in U87 cells are presented as red dots. Values for the same genes inferred from the IDH-MUT vs IDH-WT comparison in TCGA G2/G3 gliomas are overlaid as gray dots. Percentage of log2 FC direction concordance between IDH-MUT vs IDH-WT in U87 cells and glioma tumors was calculated. A number of DEGs is indicated. Black vertical line separates genes with higher expression in IDH-MUT U87 versus IDH-WT U87 from the genes with higher expression in IDH-WT U87 versus IDH-MUT U87. B Relative expression of REST in IDH-WT and IDH-MUT U87 cells at 72 h of REST silencing with siRNA. mRNA levels in transfected cells were determined with quantitative PCR and normalized to GAPDH expression in the same sample. Data are represented as mean ± SEM, n = 4 independent experiments, * p < 0.05, two-tailed Mann–Whitney test (WT: p = 0.0286; MUT: p = 0.0286). C Levels of REST protein in IDH-WT and IDH-MUT U87 cells at 72 h after transfection with control or REST specific siRNAs determined with Western blotting. Immunoblots were analyzed by densitometry. Data are represented as mean ± SEM, n = 4. ** p < 0.01 (WT: p = 0.0018, MUT: p = 0.0052; two-tailed ratio-paired t -test). No difference was observed in the level of REST protein between IDH-MUT and IDH-WT controls (siCTRL) ( p = 0.226). D Volcano plots of the genes differentially expressed between siCTRL and siREST-transfected IDH-WT (upper plot) or IDH-MUT (bottom plot) U87 glioma cells. The axes show log2 fold change (x-axis) and -log10 from adjusted q-value (y-axis). E Gene Ontology (GO) Biological Processes (BP) analysis was performed on DEGs common in IDH-WT and IDH-MUT U87 cells. The results are presented as bar plots for pathways upregulated (upper panel) and downregulated (bottom panel) in REST depleted cells

    Techniques Used: Expressing, Comparison, Transfection, Real-time Polymerase Chain Reaction, Two Tailed Test, MANN-WHITNEY, Western Blot

    REST knockdown affects invasion of glioma cells and expression of genes implicated in cell migration/invasion. A Extracellular matrix organization GO BP-related IDH-DEGs modulated by siREST (selected from functional analysis from Fig. C) presented as a heatmap for IDH-WT (left panel) and IDH-MUT (right panel) siREST (right column in each panel) vs. siCTRL (left column in each panel) U87 glioma cell lines. B Bright field microscopy images of IDH-WT and IDH-MUT U87 cells 24-, 48- and 72 h after siRNA transfection; scale bar = 200 µm. Cell viability after 24-, 48- or 72 h of REST silencing measured with a PrestoBlue assay. Data are represented as mean ± SEM, n = 3, Wilcoxon matched-pairs signed rank test, two-tailed ( p > 0.05). Dotted line at 100% denotes a viability of mock-transfected cells. C Invasiveness of IDH-WT and IDH-MUT U87 cells measured with a Matrigel invasion assay. The cells were either not treated (nt) or transfected with siCTRL or siREST. The fluorescence microscopy images (scale bar = 200 µm) show representative fields of Matrigel inserts and the bar plot shows quantification of the migrating cells. Data are presented as mean ± SEM, n = 6, * p < 0.05, Wilcoxon matched-pairs signed rank test. IDH-WT siCTRL: 908.8 ± SEM = 460; IDH-WT siREST: 1597 ± SEM = 622.3; not treated IDH-MUT: 3472 ± SEM = 324.7; not treated IDH-WT: 1019 ± SEM = 490.6; p = 0.0313. D Hierarchical clustering based on mean DNA methylation level within promoters (TSS -2000/ + 500 bps) of ECM genes whose DNA methylation was significantly different (FDR < 0.05) between IDH-MUT and G2/G3 IDH-WT tumor samples deposited in glioma Atlas. E Description as in (D) but for genes with significantly differential DNA methylation in gene bodies
    Figure Legend Snippet: REST knockdown affects invasion of glioma cells and expression of genes implicated in cell migration/invasion. A Extracellular matrix organization GO BP-related IDH-DEGs modulated by siREST (selected from functional analysis from Fig. C) presented as a heatmap for IDH-WT (left panel) and IDH-MUT (right panel) siREST (right column in each panel) vs. siCTRL (left column in each panel) U87 glioma cell lines. B Bright field microscopy images of IDH-WT and IDH-MUT U87 cells 24-, 48- and 72 h after siRNA transfection; scale bar = 200 µm. Cell viability after 24-, 48- or 72 h of REST silencing measured with a PrestoBlue assay. Data are represented as mean ± SEM, n = 3, Wilcoxon matched-pairs signed rank test, two-tailed ( p > 0.05). Dotted line at 100% denotes a viability of mock-transfected cells. C Invasiveness of IDH-WT and IDH-MUT U87 cells measured with a Matrigel invasion assay. The cells were either not treated (nt) or transfected with siCTRL or siREST. The fluorescence microscopy images (scale bar = 200 µm) show representative fields of Matrigel inserts and the bar plot shows quantification of the migrating cells. Data are presented as mean ± SEM, n = 6, * p < 0.05, Wilcoxon matched-pairs signed rank test. IDH-WT siCTRL: 908.8 ± SEM = 460; IDH-WT siREST: 1597 ± SEM = 622.3; not treated IDH-MUT: 3472 ± SEM = 324.7; not treated IDH-WT: 1019 ± SEM = 490.6; p = 0.0313. D Hierarchical clustering based on mean DNA methylation level within promoters (TSS -2000/ + 500 bps) of ECM genes whose DNA methylation was significantly different (FDR < 0.05) between IDH-MUT and G2/G3 IDH-WT tumor samples deposited in glioma Atlas. E Description as in (D) but for genes with significantly differential DNA methylation in gene bodies

    Techniques Used: Expressing, Migration, Functional Assay, Microscopy, Transfection, Prestoblue Assay, Two Tailed Test, Invasion Assay, Fluorescence, DNA Methylation Assay

    Characterization of REST ChIP-seq peaks and their target genes. A and B Ranking of the TOP 20 TF motifs identified in the sequences of the REST ChIP-seq peaks assigned to genes repressed by REST ( A ) or activated by REST ( B ). Briefly, REST expression was correlated with the genes to which REST ChIP-seq peaks were assigned using TCGA dataset (data from Fig. A). Based on the correlation results between REST gene expression and REST targets, the genes were divided into repressed or activated by REST. If correlation was statistically significant (adjusted p value < 0.05) and correlation coefficient was positive, a gene was assigned as activated by REST, while coefficient was negative, a gene was assigned as repressed by REST. C Hierarchical tree of TF motifs for enriched TF families based on PWMs. Shades of green represent motifs from TF protein families overrepresented in REST ChIP-seq peaks unique for repressed REST targets; orange-activated; magenta-motifs overrepresented in the group of motifs present in both repressed and activated REST targets. D REST and KAISO (ZBTB33) motifs clustering based on PWMs. E Hierarchical clustering of REST peaks according to the identified KAISO and REST motifs. Color-coded bars show the association of a REST peak and its target gene, impact on gene expression (repressed or activated by REST) and the presence of REST and/or KAISO motifs. F Q-value and frequency relations for selected KAISO (ZBTB33) and REST motifs within REST-ChIP-seq peaks assigned to genes activated or repressed by REST. To highlight the pattern, bar plots show the full distribution of q-values with a red dashed line indicating significance cut-off point
    Figure Legend Snippet: Characterization of REST ChIP-seq peaks and their target genes. A and B Ranking of the TOP 20 TF motifs identified in the sequences of the REST ChIP-seq peaks assigned to genes repressed by REST ( A ) or activated by REST ( B ). Briefly, REST expression was correlated with the genes to which REST ChIP-seq peaks were assigned using TCGA dataset (data from Fig. A). Based on the correlation results between REST gene expression and REST targets, the genes were divided into repressed or activated by REST. If correlation was statistically significant (adjusted p value < 0.05) and correlation coefficient was positive, a gene was assigned as activated by REST, while coefficient was negative, a gene was assigned as repressed by REST. C Hierarchical tree of TF motifs for enriched TF families based on PWMs. Shades of green represent motifs from TF protein families overrepresented in REST ChIP-seq peaks unique for repressed REST targets; orange-activated; magenta-motifs overrepresented in the group of motifs present in both repressed and activated REST targets. D REST and KAISO (ZBTB33) motifs clustering based on PWMs. E Hierarchical clustering of REST peaks according to the identified KAISO and REST motifs. Color-coded bars show the association of a REST peak and its target gene, impact on gene expression (repressed or activated by REST) and the presence of REST and/or KAISO motifs. F Q-value and frequency relations for selected KAISO (ZBTB33) and REST motifs within REST-ChIP-seq peaks assigned to genes activated or repressed by REST. To highlight the pattern, bar plots show the full distribution of q-values with a red dashed line indicating significance cut-off point

    Techniques Used: ChIP-sequencing, Expressing

    KAISO silencing affects REST-regulated genes. A Venn diagrams showing genes: 1) significantly upregulated by siKAISO; 2) significantly downregulated by siKAISO; 3) significantly upregulated by siREST; 4) significantly downregulated by siREST in IDH-MUT glioma cells. B Venn diagrams showing genes: 1) significantly upregulated by siKAISO; 2) significantly downregulated by siKAISO; 3) significantly upregulated by siREST; 4) significantly downregulated by siREST in U87 IDH-WT glioma cells. ( C ) Effect of KAISO silencing on gene expression in IDH-MUT and IDH-WT U87 glioma cells. Chi2 analysis between differentially expressed genes categories is presented in Additional File . D Effect of REST silencing on gene expression in IDH-MUT and IDH-WT U87 glioma cell lines. Chi2 analysis between differentially expressed genes categories is presented in Additional File . E Venn diagram of genes: 1) significantly upregulated by siKAISO; 2) significantly downregulated by siKAISO; 3) significantly upregulated by siREST; 4) significantly downregulated by siREST in U87 IDH-MUT glioma cells within genes from REST-repressed category. F Venn diagrams showing genes: 1) significantly upregulated by siKAISO; 2) significantly downregulated by siKAISO; 3) significantly upregulated by siREST; 4) significantly downregulated by siREST in U87 IDH-MUT glioma cells within genes from REST-activated category. G Venn diagrams showing genes: 1) significantly upregulated by siKAISO; 2) significantly downregulated by siKAISO; 3) significantly upregulated by siREST; 4) significantly downregulated by siREST in U87 IDH-WT glioma cells within genes from REST-repressed category. H Venn diagrams showing genes: 1) significantly upregulated by siKAISO; 2) significantly downregulated by siKAISO; 3) significantly upregulated by siREST; 4) significantly downregulated by siREST in U87 IDH-WT glioma cells within genes from REST-activated category. I Scatter plot of REST-repressed genes with significantly changed expression upon KAISO silencing in IDH-MUT and IDH-WT glioma cell lines. Log2 fold change in gene expression between siKAISO and siCTRL is plotted for IDH-MUT (y-axis) and IDH-WT(x-axis). The genes that had significantly changed expression in both IDH-WT and IDH-MUT are shown in black, the genes specific to IDH-MUT are shown in red, and the genes specific to IDH-WT are shown in purple. J Scatter plot of REST-activated genes with significantly changed expression upon by KAISO silencing in IDH-MUT and IDH-WT glioma cell lines. Log2 fold change in gene expression between siKAISO and /siCTRL is plotted for IDH-MUT (y-axis) and IDH-WT (x-axis). The genes that had significantly changed expression in both IDH-WT and IDH-MUT are shown in black, the genes specific to IDH-MUT are shown in red, and the genes specific to IDH-WT are shown in purple. Genes assigned to ECM organization by Gene Ontology Biological Process analysis are framed in orange
    Figure Legend Snippet: KAISO silencing affects REST-regulated genes. A Venn diagrams showing genes: 1) significantly upregulated by siKAISO; 2) significantly downregulated by siKAISO; 3) significantly upregulated by siREST; 4) significantly downregulated by siREST in IDH-MUT glioma cells. B Venn diagrams showing genes: 1) significantly upregulated by siKAISO; 2) significantly downregulated by siKAISO; 3) significantly upregulated by siREST; 4) significantly downregulated by siREST in U87 IDH-WT glioma cells. ( C ) Effect of KAISO silencing on gene expression in IDH-MUT and IDH-WT U87 glioma cells. Chi2 analysis between differentially expressed genes categories is presented in Additional File . D Effect of REST silencing on gene expression in IDH-MUT and IDH-WT U87 glioma cell lines. Chi2 analysis between differentially expressed genes categories is presented in Additional File . E Venn diagram of genes: 1) significantly upregulated by siKAISO; 2) significantly downregulated by siKAISO; 3) significantly upregulated by siREST; 4) significantly downregulated by siREST in U87 IDH-MUT glioma cells within genes from REST-repressed category. F Venn diagrams showing genes: 1) significantly upregulated by siKAISO; 2) significantly downregulated by siKAISO; 3) significantly upregulated by siREST; 4) significantly downregulated by siREST in U87 IDH-MUT glioma cells within genes from REST-activated category. G Venn diagrams showing genes: 1) significantly upregulated by siKAISO; 2) significantly downregulated by siKAISO; 3) significantly upregulated by siREST; 4) significantly downregulated by siREST in U87 IDH-WT glioma cells within genes from REST-repressed category. H Venn diagrams showing genes: 1) significantly upregulated by siKAISO; 2) significantly downregulated by siKAISO; 3) significantly upregulated by siREST; 4) significantly downregulated by siREST in U87 IDH-WT glioma cells within genes from REST-activated category. I Scatter plot of REST-repressed genes with significantly changed expression upon KAISO silencing in IDH-MUT and IDH-WT glioma cell lines. Log2 fold change in gene expression between siKAISO and siCTRL is plotted for IDH-MUT (y-axis) and IDH-WT(x-axis). The genes that had significantly changed expression in both IDH-WT and IDH-MUT are shown in black, the genes specific to IDH-MUT are shown in red, and the genes specific to IDH-WT are shown in purple. J Scatter plot of REST-activated genes with significantly changed expression upon by KAISO silencing in IDH-MUT and IDH-WT glioma cell lines. Log2 fold change in gene expression between siKAISO and /siCTRL is plotted for IDH-MUT (y-axis) and IDH-WT (x-axis). The genes that had significantly changed expression in both IDH-WT and IDH-MUT are shown in black, the genes specific to IDH-MUT are shown in red, and the genes specific to IDH-WT are shown in purple. Genes assigned to ECM organization by Gene Ontology Biological Process analysis are framed in orange

    Techniques Used: Expressing

    DNA methylation at the selected REST ChIP-seq peaks and its influence on REST targets. A DNA methylation of REST or KAISO motifs within REST ChIP-seq peaks assigned to REST-repressed targets in IDH-MUT, G2/G3 IDH-WT and G4 IDH-WT tumor samples from glioma Atlas. Description represents: REST – methylation of REST motifs of peaks lacking KAISO; REST&KAISO – methylation of REST motifs of peaks containing both REST and KAISO motifs; KAISO – methylation of KAISO motifs present in REST ChIP-seq peaks with identified KAISO but not REST motif; KAISO&REST – methylation of KAISO motifs of peaks containing both REST and KAISO motifs. B DNA methylation of REST or KAISO motifs within the REST ChIP-seq peaks assigned to REST-activated targets in IDH-MUT, G2/G3 IDH-WT and G4 IDH-WT tumor samples from glioma Atlas. Description as in A . C Distribution of REST motif DNA methylation in the REST ChIP-seq peaks containing only REST motifs and assigned to the repressed or activated REST targets based on glioma Atlas. D Distribution of REST motif DNA methylation in the REST ChIP-seq peaks containing both REST and KAISO motifs and assigned to the repressed or activated targets based on the glioma Atlas. E Cumulative distribution of DNA methylation sites (n = 601) in individual motifs. There are 601 sites containing REST or KAISO motifs with significantly different methylation among gliomas from the glioma Atlas. F Human disease pathways enriched among 47 REST targets. REST ChIP-seq peaks assigned to these targets had at least one differentially methylated REST or KAISO motif. G Description as in (F) but for REACTOME pathways. H Distribution of DNA methylation (glioma Atlas) of REST or KAISO motifs within REST ChIP-seq peaks assigned to the genes present in enriched pathways shown in F and G . I Correlation between expression of a REST-target gene and mean DNA methylation of a motif assigned to its promoter. Correlations were performed using the glioma Atlas dataset. Black squares mark REST-targets having REST and KAISO motifs in the REST ChIP-seq peaks, while white squares mark those in which only REST motifs were detected. J Correlation between expression of a REST-target gene and mean DNA methylation of its promoter in the TCGA dataset
    Figure Legend Snippet: DNA methylation at the selected REST ChIP-seq peaks and its influence on REST targets. A DNA methylation of REST or KAISO motifs within REST ChIP-seq peaks assigned to REST-repressed targets in IDH-MUT, G2/G3 IDH-WT and G4 IDH-WT tumor samples from glioma Atlas. Description represents: REST – methylation of REST motifs of peaks lacking KAISO; REST&KAISO – methylation of REST motifs of peaks containing both REST and KAISO motifs; KAISO – methylation of KAISO motifs present in REST ChIP-seq peaks with identified KAISO but not REST motif; KAISO&REST – methylation of KAISO motifs of peaks containing both REST and KAISO motifs. B DNA methylation of REST or KAISO motifs within the REST ChIP-seq peaks assigned to REST-activated targets in IDH-MUT, G2/G3 IDH-WT and G4 IDH-WT tumor samples from glioma Atlas. Description as in A . C Distribution of REST motif DNA methylation in the REST ChIP-seq peaks containing only REST motifs and assigned to the repressed or activated REST targets based on glioma Atlas. D Distribution of REST motif DNA methylation in the REST ChIP-seq peaks containing both REST and KAISO motifs and assigned to the repressed or activated targets based on the glioma Atlas. E Cumulative distribution of DNA methylation sites (n = 601) in individual motifs. There are 601 sites containing REST or KAISO motifs with significantly different methylation among gliomas from the glioma Atlas. F Human disease pathways enriched among 47 REST targets. REST ChIP-seq peaks assigned to these targets had at least one differentially methylated REST or KAISO motif. G Description as in (F) but for REACTOME pathways. H Distribution of DNA methylation (glioma Atlas) of REST or KAISO motifs within REST ChIP-seq peaks assigned to the genes present in enriched pathways shown in F and G . I Correlation between expression of a REST-target gene and mean DNA methylation of a motif assigned to its promoter. Correlations were performed using the glioma Atlas dataset. Black squares mark REST-targets having REST and KAISO motifs in the REST ChIP-seq peaks, while white squares mark those in which only REST motifs were detected. J Correlation between expression of a REST-target gene and mean DNA methylation of its promoter in the TCGA dataset

    Techniques Used: DNA Methylation Assay, ChIP-sequencing, Methylation, Expressing

    kaiso nuclear protein file name  (NanoString Technologies Inc)

     
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    kaiso  (Danaher Inc)


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    KBSs in human and mouse H19 ICR. A Human Igf2/H19 locus structure. The enlarged map shows the region of the human H19 ICR (IC1) that we previously used as a transgene. Human IC1 has repetitive structures (A-repeats 1 and 2, and B-repeats 1–7) , with a KBS (indicated as a star) located within the B4 repeat. Dots (0–7) and black boxes indicate CTCF binding sites [ , ] and Sox-Oct motifs [ , ], respectively. B Mouse Igf2/H19 locus structure. The enlarged map shows the region of the mouse H19 ICR that we previously used as a transgene. Dots (1–4) indicate CTCF-binding sites [ , ]. The black box indicates the 'b' region containing Sox-Oct motifs . The nucleotide sequence of the 118-bp region is shown below the map. RCTG motifs I–V are shown in black and white inverted. Gray boxes indicate 5ʹ- and 3ʹ-KBSs. Mutated nucleotides in Δ5- H19 ICR and the region deleted from Δ36- H19 ICR mutants are indicated below the sequence . C Nucleotide sequences of the KBSs in the human IC1 B4 repeat and in the mouse H19 ICR 118-bp region. Double-stranded DNA fragments with these sequences were used either as a probe or as competitors in ( D ). D EMSA performed on nuclear extract <t>from</t> <t>HEK293T</t> cells overexpressing FLAG-tagged <t>Kaiso</t> protein and the B4-KBS probe. Three micrograms of nuclear extract were used in lane 3 and 7 μg in the others. Two hundred- and 800-times molar excess of competitors were used
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    KBSs in human and mouse H19 ICR. A Human Igf2/H19 locus structure. The enlarged map shows the region of the human H19 ICR (IC1) that we previously used as a transgene. Human IC1 has repetitive structures (A-repeats 1 and 2, and B-repeats 1–7) , with a KBS (indicated as a star) located within the B4 repeat. Dots (0–7) and black boxes indicate CTCF binding sites [ , ] and Sox-Oct motifs [ , ], respectively. B Mouse Igf2/H19 locus structure. The enlarged map shows the region of the mouse H19 ICR that we previously used as a transgene. Dots (1–4) indicate CTCF-binding sites [ , ]. The black box indicates the 'b' region containing Sox-Oct motifs . The nucleotide sequence of the 118-bp region is shown below the map. RCTG motifs I–V are shown in black and white inverted. Gray boxes indicate 5ʹ- and 3ʹ-KBSs. Mutated nucleotides in Δ5- H19 ICR and the region deleted from Δ36- H19 ICR mutants are indicated below the sequence . C Nucleotide sequences of the KBSs in the human IC1 B4 repeat and in the mouse H19 ICR 118-bp region. Double-stranded DNA fragments with these sequences were used either as a probe or as competitors in ( D ). D EMSA performed on nuclear extract <t>from</t> <t>HEK293T</t> cells overexpressing FLAG-tagged <t>Kaiso</t> protein and the B4-KBS probe. Three micrograms of nuclear extract were used in lane 3 and 7 μg in the others. Two hundred- and 800-times molar excess of competitors were used
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    KBSs in human and mouse H19 ICR. A Human Igf2/H19 locus structure. The enlarged map shows the region of the human H19 ICR (IC1) that we previously used as a transgene. Human IC1 has repetitive structures (A-repeats 1 and 2, and B-repeats 1–7) , with a KBS (indicated as a star) located within the B4 repeat. Dots (0–7) and black boxes indicate CTCF binding sites [ , ] and Sox-Oct motifs [ , ], respectively. B Mouse Igf2/H19 locus structure. The enlarged map shows the region of the mouse H19 ICR that we previously used as a transgene. Dots (1–4) indicate CTCF-binding sites [ , ]. The black box indicates the 'b' region containing Sox-Oct motifs . The nucleotide sequence of the 118-bp region is shown below the map. RCTG motifs I–V are shown in black and white inverted. Gray boxes indicate 5ʹ- and 3ʹ-KBSs. Mutated nucleotides in Δ5- H19 ICR and the region deleted from Δ36- H19 ICR mutants are indicated below the sequence . C Nucleotide sequences of the KBSs in the human IC1 B4 repeat and in the mouse H19 ICR 118-bp region. Double-stranded DNA fragments with these sequences were used either as a probe or as competitors in ( D ). D EMSA performed on nuclear extract <t>from</t> <t>HEK293T</t> cells overexpressing FLAG-tagged <t>Kaiso</t> protein and the B4-KBS probe. Three micrograms of nuclear extract were used in lane 3 and 7 μg in the others. Two hundred- and 800-times molar excess of competitors were used
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    KBSs in human and mouse H19 ICR. A Human Igf2/H19 locus structure. The enlarged map shows the region of the human H19 ICR (IC1) that we previously used as a transgene. Human IC1 has repetitive structures (A-repeats 1 and 2, and B-repeats 1–7) , with a KBS (indicated as a star) located within the B4 repeat. Dots (0–7) and black boxes indicate CTCF binding sites [ , ] and Sox-Oct motifs [ , ], respectively. B Mouse Igf2/H19 locus structure. The enlarged map shows the region of the mouse H19 ICR that we previously used as a transgene. Dots (1–4) indicate CTCF-binding sites [ , ]. The black box indicates the 'b' region containing Sox-Oct motifs . The nucleotide sequence of the 118-bp region is shown below the map. RCTG motifs I–V are shown in black and white inverted. Gray boxes indicate 5ʹ- and 3ʹ-KBSs. Mutated nucleotides in Δ5- H19 ICR and the region deleted from Δ36- H19 ICR mutants are indicated below the sequence . C Nucleotide sequences of the KBSs in the human IC1 B4 repeat and in the mouse H19 ICR 118-bp region. Double-stranded DNA fragments with these sequences were used either as a probe or as competitors in ( D ). D EMSA performed on nuclear extract <t>from</t> <t>HEK293T</t> cells overexpressing FLAG-tagged <t>Kaiso</t> protein and the B4-KBS probe. Three micrograms of nuclear extract were used in lane 3 and 7 μg in the others. Two hundred- and 800-times molar excess of competitors were used
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    KBSs in human and mouse H19 ICR. A Human Igf2/H19 locus structure. The enlarged map shows the region of the human H19 ICR (IC1) that we previously used as a transgene. Human IC1 has repetitive structures (A-repeats 1 and 2, and B-repeats 1–7) , with a KBS (indicated as a star) located within the B4 repeat. Dots (0–7) and black boxes indicate CTCF binding sites [ , ] and Sox-Oct motifs [ , ], respectively. B Mouse Igf2/H19 locus structure. The enlarged map shows the region of the mouse H19 ICR that we previously used as a transgene. Dots (1–4) indicate CTCF-binding sites [ , ]. The black box indicates the 'b' region containing Sox-Oct motifs . The nucleotide sequence of the 118-bp region is shown below the map. RCTG motifs I–V are shown in black and white inverted. Gray boxes indicate 5ʹ- and 3ʹ-KBSs. Mutated nucleotides in Δ5- H19 ICR and the region deleted from Δ36- H19 ICR mutants are indicated below the sequence . C Nucleotide sequences of the KBSs in the human IC1 B4 repeat and in the mouse H19 ICR 118-bp region. Double-stranded DNA fragments with these sequences were used either as a probe or as competitors in ( D ). D EMSA performed on nuclear extract <t>from</t> <t>HEK293T</t> cells overexpressing FLAG-tagged <t>Kaiso</t> protein and the B4-KBS probe. Three micrograms of nuclear extract were used in lane 3 and 7 μg in the others. Two hundred- and 800-times molar excess of competitors were used
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    KBSs in human and mouse H19 ICR. A Human Igf2/H19 locus structure. The enlarged map shows the region of the human H19 ICR (IC1) that we previously used as a transgene. Human IC1 has repetitive structures (A-repeats 1 and 2, and B-repeats 1–7) , with a KBS (indicated as a star) located within the B4 repeat. Dots (0–7) and black boxes indicate CTCF binding sites [ , ] and Sox-Oct motifs [ , ], respectively. B Mouse Igf2/H19 locus structure. The enlarged map shows the region of the mouse H19 ICR that we previously used as a transgene. Dots (1–4) indicate CTCF-binding sites [ , ]. The black box indicates the 'b' region containing Sox-Oct motifs . The nucleotide sequence of the 118-bp region is shown below the map. RCTG motifs I–V are shown in black and white inverted. Gray boxes indicate 5ʹ- and 3ʹ-KBSs. Mutated nucleotides in Δ5- H19 ICR and the region deleted from Δ36- H19 ICR mutants are indicated below the sequence . C Nucleotide sequences of the KBSs in the human IC1 B4 repeat and in the mouse H19 ICR 118-bp region. Double-stranded DNA fragments with these sequences were used either as a probe or as competitors in ( D ). D EMSA performed on nuclear extract <t>from</t> <t>HEK293T</t> cells overexpressing FLAG-tagged <t>Kaiso</t> protein and the B4-KBS probe. Three micrograms of nuclear extract were used in lane 3 and 7 μg in the others. Two hundred- and 800-times molar excess of competitors were used
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    KBSs in human and mouse H19 ICR. A Human Igf2/H19 locus structure. The enlarged map shows the region of the human H19 ICR (IC1) that we previously used as a transgene. Human IC1 has repetitive structures (A-repeats 1 and 2, and B-repeats 1–7) , with a KBS (indicated as a star) located within the B4 repeat. Dots (0–7) and black boxes indicate CTCF binding sites [ , ] and Sox-Oct motifs [ , ], respectively. B Mouse Igf2/H19 locus structure. The enlarged map shows the region of the mouse H19 ICR that we previously used as a transgene. Dots (1–4) indicate CTCF-binding sites [ , ]. The black box indicates the 'b' region containing Sox-Oct motifs . The nucleotide sequence of the 118-bp region is shown below the map. RCTG motifs I–V are shown in black and white inverted. Gray boxes indicate 5ʹ- and 3ʹ-KBSs. Mutated nucleotides in Δ5- H19 ICR and the region deleted from Δ36- H19 ICR mutants are indicated below the sequence . C Nucleotide sequences of the KBSs in the human IC1 B4 repeat and in the mouse H19 ICR 118-bp region. Double-stranded DNA fragments with these sequences were used either as a probe or as competitors in ( D ). D EMSA performed on nuclear extract <t>from</t> <t>HEK293T</t> cells overexpressing FLAG-tagged <t>Kaiso</t> protein and the B4-KBS probe. Three micrograms of nuclear extract were used in lane 3 and 7 μg in the others. Two hundred- and 800-times molar excess of competitors were used
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    KBSs in human and mouse H19 ICR. A Human Igf2/H19 locus structure. The enlarged map shows the region of the human H19 ICR (IC1) that we previously used as a transgene. Human IC1 has repetitive structures (A-repeats 1 and 2, and B-repeats 1–7) , with a KBS (indicated as a star) located within the B4 repeat. Dots (0–7) and black boxes indicate CTCF binding sites [ , ] and Sox-Oct motifs [ , ], respectively. B Mouse Igf2/H19 locus structure. The enlarged map shows the region of the mouse H19 ICR that we previously used as a transgene. Dots (1–4) indicate CTCF-binding sites [ , ]. The black box indicates the 'b' region containing Sox-Oct motifs . The nucleotide sequence of the 118-bp region is shown below the map. RCTG motifs I–V are shown in black and white inverted. Gray boxes indicate 5ʹ- and 3ʹ-KBSs. Mutated nucleotides in Δ5- H19 ICR and the region deleted from Δ36- H19 ICR mutants are indicated below the sequence . C Nucleotide sequences of the KBSs in the human IC1 B4 repeat and in the mouse H19 ICR 118-bp region. Double-stranded DNA fragments with these sequences were used either as a probe or as competitors in ( D ). D EMSA performed on nuclear extract <t>from</t> <t>HEK293T</t> cells overexpressing FLAG-tagged <t>Kaiso</t> protein and the B4-KBS probe. Three micrograms of nuclear extract were used in lane 3 and 7 μg in the others. Two hundred- and 800-times molar excess of competitors were used
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    KBSs in human and mouse H19 ICR. A Human Igf2/H19 locus structure. The enlarged map shows the region of the human H19 ICR (IC1) that we previously used as a transgene. Human IC1 has repetitive structures (A-repeats 1 and 2, and B-repeats 1–7) , with a KBS (indicated as a star) located within the B4 repeat. Dots (0–7) and black boxes indicate CTCF binding sites [ , ] and Sox-Oct motifs [ , ], respectively. B Mouse Igf2/H19 locus structure. The enlarged map shows the region of the mouse H19 ICR that we previously used as a transgene. Dots (1–4) indicate CTCF-binding sites [ , ]. The black box indicates the 'b' region containing Sox-Oct motifs . The nucleotide sequence of the 118-bp region is shown below the map. RCTG motifs I–V are shown in black and white inverted. Gray boxes indicate 5ʹ- and 3ʹ-KBSs. Mutated nucleotides in Δ5- H19 ICR and the region deleted from Δ36- H19 ICR mutants are indicated below the sequence . C Nucleotide sequences of the KBSs in the human IC1 B4 repeat and in the mouse H19 ICR 118-bp region. Double-stranded DNA fragments with these sequences were used either as a probe or as competitors in ( D ). D EMSA performed on nuclear extract from HEK293T cells overexpressing FLAG-tagged Kaiso protein and the B4-KBS probe. Three micrograms of nuclear extract were used in lane 3 and 7 μg in the others. Two hundred- and 800-times molar excess of competitors were used

    Journal: Epigenetics & Chromatin

    Article Title: Imprinted DNA methylation of the H19 ICR is established and maintained in vivo in the absence of Kaiso

    doi: 10.1186/s13072-024-00544-8

    Figure Lengend Snippet: KBSs in human and mouse H19 ICR. A Human Igf2/H19 locus structure. The enlarged map shows the region of the human H19 ICR (IC1) that we previously used as a transgene. Human IC1 has repetitive structures (A-repeats 1 and 2, and B-repeats 1–7) , with a KBS (indicated as a star) located within the B4 repeat. Dots (0–7) and black boxes indicate CTCF binding sites [ , ] and Sox-Oct motifs [ , ], respectively. B Mouse Igf2/H19 locus structure. The enlarged map shows the region of the mouse H19 ICR that we previously used as a transgene. Dots (1–4) indicate CTCF-binding sites [ , ]. The black box indicates the 'b' region containing Sox-Oct motifs . The nucleotide sequence of the 118-bp region is shown below the map. RCTG motifs I–V are shown in black and white inverted. Gray boxes indicate 5ʹ- and 3ʹ-KBSs. Mutated nucleotides in Δ5- H19 ICR and the region deleted from Δ36- H19 ICR mutants are indicated below the sequence . C Nucleotide sequences of the KBSs in the human IC1 B4 repeat and in the mouse H19 ICR 118-bp region. Double-stranded DNA fragments with these sequences were used either as a probe or as competitors in ( D ). D EMSA performed on nuclear extract from HEK293T cells overexpressing FLAG-tagged Kaiso protein and the B4-KBS probe. Three micrograms of nuclear extract were used in lane 3 and 7 μg in the others. Two hundred- and 800-times molar excess of competitors were used

    Article Snippet: Nuclear extracts were prepared from HEK293T cells overexpressing FLAG-tagged Kaiso protein using the Nuclear Extract Kit (Active Motif).

    Techniques: Binding Assay, Sequencing