anti 3xflag  (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: Generation and validation of a system for rapid depletion of ZFP143 in mESCs (A) Schematic representation of the dTAG degron system. The endogenous Zfp143 locus is modified to create a fusion with the FKBP12 F36V -2xHA-P2A-eGFP cassette. (B) Western blot analysis of ZFP143 levels with an antibody against the endogenous ZFP143 at different time points after dTAG-V1 treatment. (C) Western blot analysis of ZFP143 levels with an antibody against the HA tag at different time points after dTAG-V1 treatment. (D) Tornado plots showing ZFP143-HA ChIP-seq signal centered at ZFP143-HA peaks in DMSO- and dTAG-V1-treated cells. (E) Genomic tracks showing ZFP143-HA ChIP-seq (red) and TT-seq nascent transcription (yellow for sense and purple for antisense transcription) at Rpp30 and Pomgnt2 in DMSO-treated and dTAG-V1-treated cells. (F) Fraction of ZFP143-bound genes among downregulated (green), upregulated (pink), and stable (gray) genes in the TT-seq at different time points after ZFP143 depletion.

Article Snippet: To further explore the overlap between ZNF143 and CTCF, we compared ChIP-seq data generated using the Proteintech antibody (anti-ZNF143) with C-terminally 3xFLAG-tagged ZNF143 ChIP-seq (anti-FLAG-ZNF143) in K562 cells.

Techniques: Biomarker Discovery, Modification, Western Blot, 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: 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: To further explore the overlap between ZNF143 and CTCF, we compared ChIP-seq data generated using the Proteintech antibody (anti-ZNF143) with C-terminally 3xFLAG-tagged ZNF143 ChIP-seq (anti-FLAG-ZNF143) in K562 cells.

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: To further explore the overlap between ZNF143 and CTCF, we compared ChIP-seq data generated using the Proteintech antibody (anti-ZNF143) with C-terminally 3xFLAG-tagged ZNF143 ChIP-seq (anti-FLAG-ZNF143) 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: To further explore the overlap between ZNF143 and CTCF, we compared ChIP-seq data generated using the Proteintech antibody (anti-ZNF143) with C-terminally 3xFLAG-tagged ZNF143 ChIP-seq (anti-FLAG-ZNF143) in K562 cells.

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