znf143 peaks  (Proteintech)

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: 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.

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: 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.

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

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: ZFP143 depletion has no detectable effect on 3D genome structure and CTCF binding (A) Average Hi-C loops in DMSO-treated and dTAG-V1-treated cells. Value in the upper-right corner indicates the interaction strength of the loop over the background. (B) Same as in (A), but for the average ZFP143-associated Hi-C loops. (C) 4C-seq data generated for the Cpox and Cldn1 (left) and Zfp111 and Zfp108 (right) loci. The matrix in the top panel represents interaction frequencies in a previously published high-resolution Micro-C dataset. The arrows point to detected Micro-C chromatin loops. The bottom panel shows 4C contact profiles in DMSO-treated (blue) and dTAG-V1-treated (orange) cells. Genomic tracks show ZFP143-HA ChIP-seq (red), calibrated CTCF ChIP-seq (blue), TT-seq nascent transcription (yellow for sense and purple for antisense transcription) in DMSO-treated and dTAG-V1-treated cells. (D) Tornado plots of calibrated CTCF ChIP-seq signal centered at CTCF peaks in DMSO-treated and dTAG-V1-treated cells. (E) Genomic tracks showing ZFP143-HA ChIP-seq (red) in DMSO-treated cells and calibrated CTCF ChIP-seq (blue) in DMSO-treated and dTAG-V1-treated cells. (F) Venn diagram showing the overlap between ZFP143-HA (red) and CTCF (blue) peaks.

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: Binding Assay, Hi-C, Generated, ChIP-sequencing

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