Journal: Molecular Cell

Article Title: ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF

doi: 10.1016/j.molcel.2024.11.031

Figure Lengend Snippet: Re-analysis of publicly available ChIP-seq data reveals ZNF143 antibody cross-reactivity with CTCF (A) Overlap between ZNF143 peaks from re-analyzed publicly available data and CTCF peaks from CISTROME for human (left) and mouse (right) datasets. Each dot represents the overlap between the indicated ZNF143 peak set with an individual CTCF peak set. Colors represent the antibody used for chromatin immunoprecipitation. (B) Venn diagram showing the overlap between ZNF143 peaks detected by Proteintech (light pink) and FLAG (light green) antibodies in K562 cells. (C) Heatmap showing the enrichment of ZNF143 SBS and CTCF motifs in common, Proteintech-specific, and FLAG-specific peaks in K562 cells. (D) Tornado plots of ChIP-seq signals detected by Proteintech (light pink), FLAG (light green), and custom (orange) antibodies, and CTCF signal (blue) in K562 cells. The ChIP-seq signals are centered on common (top) and Proteintech-specific (bottom) peaks. (E) Genomic tracks showing ChIP-seq signals for CTCF (blue) and signals detected by Proteintech (pink), FLAG (light green), and custom (orange) antibodies in K562 cells. Rectangles indicate common (left) and Proteintech-specific (middle and right) peaks in the region. (F) Scatterplot of the percentage of loop anchors overlapping the peak (x axis) against the fold enrichment of peaks in loop anchors (y axis) for a number of DNA-binding proteins and for Proteintech-specific, FLAG-specific, and common peaks in K562 cells.

Article Snippet: The datasets that showed the greatest overlap with CTCF peaks were obtained using the same antibody, anti-ZNF143 Proteintech 16618-1-AP (hereafter referred to as Proteintech), a polyclonal antibody that recognizes endogenous ZNF143 protein.

Techniques: ChIP-sequencing, Chromatin Immunoprecipitation, DNA Binding Assay

Journal: Molecular Cell

Article Title: ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF

doi: 10.1016/j.molcel.2024.11.031

Figure Lengend Snippet:

Article Snippet: The datasets that showed the greatest overlap with CTCF peaks were obtained using the same antibody, anti-ZNF143 Proteintech 16618-1-AP (hereafter referred to as Proteintech), a polyclonal antibody that recognizes endogenous ZNF143 protein.

Techniques: Virus, Bacteria, Recombinant, Western Blot, Flow Cytometry, Purification, Plasmid Preparation, Bradford Protein Assay, Multiplex Assay, Microscopy, Cell Counting, Software

Journal: BMC Genomics

Article Title: The role of ZNF143 overexpression in rat liver cell proliferation

doi: 10.1186/s12864-022-08714-2

Figure Lengend Snippet: The expression of ZNF143 is upregulated during the proliferation phase of liver regeneration. A mRNA microarray data showing the relative expression level of ZNF143 during liver regeneration ( n = 3 per time point in each group). B Western blot analyses showing ZNF143 protein level at 0 h, 2 h and 24 h during liver regeneration. Three biological replicates were analyzed. C IHC analyses showing the expression of ZNF143 in liver tissue during the proliferation phase of liver regeneration. The data are presented as mean ± SD. P values: * P < 0.05; ** P < 0.01 using two-tailed Student t test ( A , B )

Article Snippet: Antibodies used in this study were anti-ZNF143 (Proteintech, 16,618–1-AP, 1:1000), anti-β-actin (Cell Signaling Technology, #4967S, 1:2000), anti-Lamin A/C(ThermoFisher, MA1-06,102, 1:1000), anti-GAPDH (Cell Signaling Technology, #8884S, 1:2000).

Techniques: Expressing, Microarray, Western Blot, Two Tailed Test

Journal: BMC Genomics

Article Title: The role of ZNF143 overexpression in rat liver cell proliferation

doi: 10.1186/s12864-022-08714-2

Figure Lengend Snippet: ZNF143 OE significant inhibition of BRL-3A cell proliferation and cell cycle progression. A qRT-PCR analyses showing ZNF143 mRNA level after OE For each qRT-PCR experiment, three biological replicates and three technical replicates were analyzed. β-actin was used as an internal reference gene. B Western blot analyses showing ZNF143 protein level after OE. Two biological replicates and three technical replicates were analyzed. C CCK-8 assay analyses showing cell proliferation 24 h, 48 h, and 72 h after ZNF143 OE. For each CCK-8 assay, three biological replicates were analyzed. D GO (RNA-seq) enrichment analyses showing cell biological pathways enriched 72 h after OE. The data are presented as mean ± SD. P values: * P < 0.05; ** P < 0.01 using two-tailed Student t test ( A , B , C ); FDR ≤ 0.05 ( D )

Article Snippet: Antibodies used in this study were anti-ZNF143 (Proteintech, 16,618–1-AP, 1:1000), anti-β-actin (Cell Signaling Technology, #4967S, 1:2000), anti-Lamin A/C(ThermoFisher, MA1-06,102, 1:1000), anti-GAPDH (Cell Signaling Technology, #8884S, 1:2000).

Techniques: Inhibition, Quantitative RT-PCR, Western Blot, CCK-8 Assay, RNA Sequencing Assay, Two Tailed Test

Journal: BMC Genomics

Article Title: The role of ZNF143 overexpression in rat liver cell proliferation

doi: 10.1186/s12864-022-08714-2

Figure Lengend Snippet: Genome-wide BS distribution analysis of ZNF143 after OE. A Heatmap showing the changes of ZNF143 and CTCF BSs after ZNF143 OE (FDR < 0.1, log 2 FoldChange > 0.5). B Genome-wide peak annotation showing the proportion of exon, intron, promoter, TSS and intergenic region after ZNF143 OE. C Differential peak annotation showing the proportion of exon, intron, promoter, TSS and intergenic region after ZNF143 OE

Article Snippet: Antibodies used in this study were anti-ZNF143 (Proteintech, 16,618–1-AP, 1:1000), anti-β-actin (Cell Signaling Technology, #4967S, 1:2000), anti-Lamin A/C(ThermoFisher, MA1-06,102, 1:1000), anti-GAPDH (Cell Signaling Technology, #8884S, 1:2000).

Techniques: Genome Wide

Journal: BMC Genomics

Article Title: The role of ZNF143 overexpression in rat liver cell proliferation

doi: 10.1186/s12864-022-08714-2

Figure Lengend Snippet: DEGs regulation analysis using integrated ChIP-seq and RNA-seq data. A The correlation between ZNF143 differential BSs and DEGs after ZNF143 OE. The red dot represents genes with significant differential expression (FDR < 0.05, log 2 FoldChange > 0.5) and significant differential binding (log 2 FoldChange > 0.5). Numbers within plots denote the percentage of genes in the respective quadrants. B Correlation network analysis of the DEGs (FDR < 0.01, log 2 FoldChange > 1.0). The black dot represents genes with significant differential binding (log 2 FoldChange > 0.5). C GO enrichment analysis of genes in ( B )

Article Snippet: Antibodies used in this study were anti-ZNF143 (Proteintech, 16,618–1-AP, 1:1000), anti-β-actin (Cell Signaling Technology, #4967S, 1:2000), anti-Lamin A/C(ThermoFisher, MA1-06,102, 1:1000), anti-GAPDH (Cell Signaling Technology, #8884S, 1:2000).

Techniques: ChIP-sequencing, RNA Sequencing Assay, Expressing, Binding Assay

Journal: BMC Genomics

Article Title: The role of ZNF143 overexpression in rat liver cell proliferation

doi: 10.1186/s12864-022-08714-2

Figure Lengend Snippet: The expression of ZNF143 is upregulated during the proliferation phase of liver regeneration. A mRNA microarray data showing the relative expression level of ZNF143 during liver regeneration ( n = 3 per time point in each group). B Western blot analyses showing ZNF143 protein level at 0 h, 2 h and 24 h during liver regeneration. Three biological replicates were analyzed. C IHC analyses showing the expression of ZNF143 in liver tissue during the proliferation phase of liver regeneration. The data are presented as mean ± SD. P values: * P < 0.05; ** P < 0.01 using two-tailed Student t test ( A , B )

Article Snippet: Tissue sections were then incubated in humidified chamber for over 16 h at 4 °C with ZNF143 primary antibody (Proteintech, 16,618–1-AP) (1:100 in TBST).

Techniques: Expressing, Microarray, Western Blot, Two Tailed Test

Journal: BMC Genomics

Article Title: The role of ZNF143 overexpression in rat liver cell proliferation

doi: 10.1186/s12864-022-08714-2

Figure Lengend Snippet: ZNF143 OE significant inhibition of BRL-3A cell proliferation and cell cycle progression. A qRT-PCR analyses showing ZNF143 mRNA level after OE For each qRT-PCR experiment, three biological replicates and three technical replicates were analyzed. β-actin was used as an internal reference gene. B Western blot analyses showing ZNF143 protein level after OE. Two biological replicates and three technical replicates were analyzed. C CCK-8 assay analyses showing cell proliferation 24 h, 48 h, and 72 h after ZNF143 OE. For each CCK-8 assay, three biological replicates were analyzed. D GO (RNA-seq) enrichment analyses showing cell biological pathways enriched 72 h after OE. The data are presented as mean ± SD. P values: * P < 0.05; ** P < 0.01 using two-tailed Student t test ( A , B , C ); FDR ≤ 0.05 ( D )

Article Snippet: Tissue sections were then incubated in humidified chamber for over 16 h at 4 °C with ZNF143 primary antibody (Proteintech, 16,618–1-AP) (1:100 in TBST).

Techniques: Inhibition, Quantitative RT-PCR, Western Blot, CCK-8 Assay, RNA Sequencing Assay, Two Tailed Test

Journal: BMC Genomics

Article Title: The role of ZNF143 overexpression in rat liver cell proliferation

doi: 10.1186/s12864-022-08714-2

Figure Lengend Snippet: Genome-wide BS distribution analysis of ZNF143 after OE. A Heatmap showing the changes of ZNF143 and CTCF BSs after ZNF143 OE (FDR < 0.1, log 2 FoldChange > 0.5). B Genome-wide peak annotation showing the proportion of exon, intron, promoter, TSS and intergenic region after ZNF143 OE. C Differential peak annotation showing the proportion of exon, intron, promoter, TSS and intergenic region after ZNF143 OE

Article Snippet: Tissue sections were then incubated in humidified chamber for over 16 h at 4 °C with ZNF143 primary antibody (Proteintech, 16,618–1-AP) (1:100 in TBST).

Techniques: Genome Wide

Journal: BMC Genomics

Article Title: The role of ZNF143 overexpression in rat liver cell proliferation

doi: 10.1186/s12864-022-08714-2

Figure Lengend Snippet: DEGs regulation analysis using integrated ChIP-seq and RNA-seq data. A The correlation between ZNF143 differential BSs and DEGs after ZNF143 OE. The red dot represents genes with significant differential expression (FDR < 0.05, log 2 FoldChange > 0.5) and significant differential binding (log 2 FoldChange > 0.5). Numbers within plots denote the percentage of genes in the respective quadrants. B Correlation network analysis of the DEGs (FDR < 0.01, log 2 FoldChange > 1.0). The black dot represents genes with significant differential binding (log 2 FoldChange > 0.5). C GO enrichment analysis of genes in ( B )

Article Snippet: Tissue sections were then incubated in humidified chamber for over 16 h at 4 °C with ZNF143 primary antibody (Proteintech, 16,618–1-AP) (1:100 in TBST).

Techniques: ChIP-sequencing, RNA Sequencing Assay, Expressing, Binding Assay

Journal: BMC Genomics

Article Title: The role of ZNF143 overexpression in rat liver cell proliferation

doi: 10.1186/s12864-022-08714-2

Figure Lengend Snippet: The expression of ZNF143 is upregulated during the proliferation phase of liver regeneration. A mRNA microarray data showing the relative expression level of ZNF143 during liver regeneration ( n = 3 per time point in each group). B Western blot analyses showing ZNF143 protein level at 0 h, 2 h and 24 h during liver regeneration. Three biological replicates were analyzed. C IHC analyses showing the expression of ZNF143 in liver tissue during the proliferation phase of liver regeneration. The data are presented as mean ± SD. P values: * P < 0.05; ** P < 0.01 using two-tailed Student t test ( A , B )

Article Snippet: The primary antibody of ZNF143 (Proteintech, 16,618–1-AP) or CTCF (Millipore, 07–729) was diluted 1:50 in 50 μL of Dig-Wash buffer and then incubated on a rotator overnight at 4 °C.

Techniques: Expressing, Microarray, Western Blot, Two Tailed Test

Journal: BMC Genomics

Article Title: The role of ZNF143 overexpression in rat liver cell proliferation

doi: 10.1186/s12864-022-08714-2

Figure Lengend Snippet: ZNF143 OE significant inhibition of BRL-3A cell proliferation and cell cycle progression. A qRT-PCR analyses showing ZNF143 mRNA level after OE For each qRT-PCR experiment, three biological replicates and three technical replicates were analyzed. β-actin was used as an internal reference gene. B Western blot analyses showing ZNF143 protein level after OE. Two biological replicates and three technical replicates were analyzed. C CCK-8 assay analyses showing cell proliferation 24 h, 48 h, and 72 h after ZNF143 OE. For each CCK-8 assay, three biological replicates were analyzed. D GO (RNA-seq) enrichment analyses showing cell biological pathways enriched 72 h after OE. The data are presented as mean ± SD. P values: * P < 0.05; ** P < 0.01 using two-tailed Student t test ( A , B , C ); FDR ≤ 0.05 ( D )

Article Snippet: The primary antibody of ZNF143 (Proteintech, 16,618–1-AP) or CTCF (Millipore, 07–729) was diluted 1:50 in 50 μL of Dig-Wash buffer and then incubated on a rotator overnight at 4 °C.

Techniques: Inhibition, Quantitative RT-PCR, Western Blot, CCK-8 Assay, RNA Sequencing Assay, Two Tailed Test

Journal: BMC Genomics

Article Title: The role of ZNF143 overexpression in rat liver cell proliferation

doi: 10.1186/s12864-022-08714-2

Figure Lengend Snippet: Genome-wide BS distribution analysis of ZNF143 after OE. A Heatmap showing the changes of ZNF143 and CTCF BSs after ZNF143 OE (FDR < 0.1, log 2 FoldChange > 0.5). B Genome-wide peak annotation showing the proportion of exon, intron, promoter, TSS and intergenic region after ZNF143 OE. C Differential peak annotation showing the proportion of exon, intron, promoter, TSS and intergenic region after ZNF143 OE

Article Snippet: The primary antibody of ZNF143 (Proteintech, 16,618–1-AP) or CTCF (Millipore, 07–729) was diluted 1:50 in 50 μL of Dig-Wash buffer and then incubated on a rotator overnight at 4 °C.

Techniques: Genome Wide

Journal: BMC Genomics

Article Title: The role of ZNF143 overexpression in rat liver cell proliferation

doi: 10.1186/s12864-022-08714-2

Figure Lengend Snippet: DEGs regulation analysis using integrated ChIP-seq and RNA-seq data. A The correlation between ZNF143 differential BSs and DEGs after ZNF143 OE. The red dot represents genes with significant differential expression (FDR < 0.05, log 2 FoldChange > 0.5) and significant differential binding (log 2 FoldChange > 0.5). Numbers within plots denote the percentage of genes in the respective quadrants. B Correlation network analysis of the DEGs (FDR < 0.01, log 2 FoldChange > 1.0). The black dot represents genes with significant differential binding (log 2 FoldChange > 0.5). C GO enrichment analysis of genes in ( B )

Article Snippet: The primary antibody of ZNF143 (Proteintech, 16,618–1-AP) or CTCF (Millipore, 07–729) was diluted 1:50 in 50 μL of Dig-Wash buffer and then incubated on a rotator overnight at 4 °C.

Techniques: ChIP-sequencing, RNA Sequencing Assay, Expressing, Binding Assay