ctcf chip seq signal  (Proteintech)

Journal: Cell genomics

Article Title: Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation.

doi: 10.1016/j.xgen.2025.100813

Figure Lengend Snippet: Figure 1. CTCF complementation system (A) Scheme of the CTCF doxycycline-inducible degron system. (B) Experimental strategy for the expression of WT and mutant transgenic CTCF. (C) Flow cytometry showing the level of GFP (endogenous CTCF) and mRuby (transgenic WT CTCF). (D) Left, scheme showing the locations of the different types of CTCF mutations within a ZF. Amino acids making contacts with the DNA are shown in shades of pink, residues that coordinate the zinc ion in red, boundary residues in purple, and residues that contact the sugar phosphate backbone of DNA in blue. Right, representation of CTCF showing the locations of each mutation under investigation. (legend continued on next page)

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies mouse anti FLAG Sigma Cat#F1804; RRID: AB_262044 mouse anti GAPDH BioLegend Cat#607901 (clone W17079A); RRID:AB_2734502 mouse anti CTCF (WB) Active Motif Cat#61311; RRID: AB_2614975 mouse anti CTCF (Chip-seq) Cell signaling Cat#3418, RRID: AB_2086791 FLAG M2 Magnetic Beads Sigma Cat#M8823; RRID: AB_2637089 mouse anti SMC3 abcam Cat#ab9263; RRID: AB_307122 Mouse anti RAD21 abcam Cat#ab992; RRID: AB_2176601 Mouse anti SMC1 ThermoFisher Cat#MA5-15583; RRID: AB_10980475 Rabbit IgG abcam Cat#ab37415; RRID: AB_2631996 Critical commercial assays Tagment DNA Enzyme and Buffer Kit Illumina Cat#20034198 Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Cat#20040529 Arima Hi-C kit Arima Cat#A510008 Oligonucleotide Nextera barcodes Schmidl et al.53 N/A Deposited data RNA-seq This paper GEO: GSE270669 HiC This paper GEO: GSE270669 OmniATAC-seq This paper GEO: GSE270669 SMC3 Chipmentation This paper GEO: GSE270669 FLAG Chipmentation This paper GEO: GSE270669 H3K27ac peaks from 120/Ola mESCs ENCODE ENCODE: ENCFF519QMV HOCOMOCO v11 Kulakovskiy et al.54 https://hocomoco11.autosome.org/ Developmental germ layer gene sets Hutchins et al.55 N/A CTCF associated NDD genes Konrad et al.9 N/A Developmental genes DECIPHER https://www.deciphergenomics.org/ddd/overview Imprinted genes geneimprint https://www.geneimprint.com/ ENCODE blacklisted regions Amemiya et al.56 https://github.com/Boyle-Lab/Blacklist KEGG genesets Kanehisa et al.32 https://www.genome.jp/kegg/genes.html CTCF-DNA complex (WT ZF1-7) PDB PDB: 8SSS CTCF-DNA complex (K365T ZF1-7) PDB PDB: 8SST CTCF-DNA complex (WT ZF3-11) PDB PDB: 8SSQ CTCF-DNA complex (K365T ZF3-11) PDB PDB: 8SSR Experimental models: Cell lines Mouse embryonic stem cells E14Tg2a (129/Ola isogenic background) expressing transgene WT or mutant CTCF This paper N/A pEN366 - pTRE3G-CTCF-mRuby2BGHpA-CAGGS-rtta3G-rbgpA-FrtPGK-EM7-PuroR-bpA-Frt TIGRE donor Nora et al.15 Addgene #156432 pX330-EN1201 Nora et al.15 Addgene #92144 (Continued on next page) e1 Cell Genomics 5, 100813, April 9, 2025

Techniques: Expressing, Mutagenesis, Transgenic Assay, Flow Cytometry

Journal: Cell genomics

Article Title: Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation.

doi: 10.1016/j.xgen.2025.100813

Figure Lengend Snippet: Figure 3. Each mutation uniquely impacts CTCF’s chromatin bound fraction, residence time, and interaction with DNA (A) Plots of FRAP dynamics for WT and mutant CTCF. The bold lines show the fitted model of the average recovery, and the outlines give the 95% confidence intervals (95% CIs). (B) Violin plots of specific bound fractions. (C) Violin plots of specific residence times (min). p values were determined by bootstrapping (n = 2,500). (D) Heatmaps show the proportion of CTCF-cohesin versus CTCF-only binding sites. UN corresponds to the FLAG control in untreated cells. (E) Correlation between residence time and the percentage of CTCF-cohesin overlap. (F) Correlation between the FRAP-specific bound fraction relative to WT and the fraction of common CTCF sites relative to all potential binding sites. (G) Correlation between the FRAP-specific bound fraction relative to WT and the effect of CTCF binding on ATAC-seq signal at CTCF-SMC3 sites (Figure 2B). For (E)–(G), data were generated in 2 replicates, the p values were calculated using linear regression, and the shaded area corresponds to the 95% CI. See also Figures S10–S14.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies mouse anti FLAG Sigma Cat#F1804; RRID: AB_262044 mouse anti GAPDH BioLegend Cat#607901 (clone W17079A); RRID:AB_2734502 mouse anti CTCF (WB) Active Motif Cat#61311; RRID: AB_2614975 mouse anti CTCF (Chip-seq) Cell signaling Cat#3418, RRID: AB_2086791 FLAG M2 Magnetic Beads Sigma Cat#M8823; RRID: AB_2637089 mouse anti SMC3 abcam Cat#ab9263; RRID: AB_307122 Mouse anti RAD21 abcam Cat#ab992; RRID: AB_2176601 Mouse anti SMC1 ThermoFisher Cat#MA5-15583; RRID: AB_10980475 Rabbit IgG abcam Cat#ab37415; RRID: AB_2631996 Critical commercial assays Tagment DNA Enzyme and Buffer Kit Illumina Cat#20034198 Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Cat#20040529 Arima Hi-C kit Arima Cat#A510008 Oligonucleotide Nextera barcodes Schmidl et al.53 N/A Deposited data RNA-seq This paper GEO: GSE270669 HiC This paper GEO: GSE270669 OmniATAC-seq This paper GEO: GSE270669 SMC3 Chipmentation This paper GEO: GSE270669 FLAG Chipmentation This paper GEO: GSE270669 H3K27ac peaks from 120/Ola mESCs ENCODE ENCODE: ENCFF519QMV HOCOMOCO v11 Kulakovskiy et al.54 https://hocomoco11.autosome.org/ Developmental germ layer gene sets Hutchins et al.55 N/A CTCF associated NDD genes Konrad et al.9 N/A Developmental genes DECIPHER https://www.deciphergenomics.org/ddd/overview Imprinted genes geneimprint https://www.geneimprint.com/ ENCODE blacklisted regions Amemiya et al.56 https://github.com/Boyle-Lab/Blacklist KEGG genesets Kanehisa et al.32 https://www.genome.jp/kegg/genes.html CTCF-DNA complex (WT ZF1-7) PDB PDB: 8SSS CTCF-DNA complex (K365T ZF1-7) PDB PDB: 8SST CTCF-DNA complex (WT ZF3-11) PDB PDB: 8SSQ CTCF-DNA complex (K365T ZF3-11) PDB PDB: 8SSR Experimental models: Cell lines Mouse embryonic stem cells E14Tg2a (129/Ola isogenic background) expressing transgene WT or mutant CTCF This paper N/A pEN366 - pTRE3G-CTCF-mRuby2BGHpA-CAGGS-rtta3G-rbgpA-FrtPGK-EM7-PuroR-bpA-Frt TIGRE donor Nora et al.15 Addgene #156432 pX330-EN1201 Nora et al.15 Addgene #92144 (Continued on next page) e1 Cell Genomics 5, 100813, April 9, 2025

Techniques: Mutagenesis, Binding Assay, Control, Generated

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 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.

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 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.

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 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.

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