dtag 7  (MedChemExpress)

Journal: Cell Genomics

Article Title: Long-range enhancer-controlled genes are hypersensitive to regulatory factor perturbations

doi: 10.1016/j.xgen.2025.100778

Figure Lengend Snippet:

Article Snippet: dTAG7 , TOCRIS , Cat#6912.

Techniques: Virus, Recombinant, Isolation, Western Blot, Construct, Software, Sequencing, Flow Cytometry

Journal: Cell Genomics

Article Title: Long-range enhancer-controlled genes are hypersensitive to regulatory factor perturbations

doi: 10.1016/j.xgen.2025.100778

Figure Lengend Snippet: Regulation of distal-enhancer connected genes by mediator and LDB1 (A and B) Cumulative distribution curves of log2FCs of enhancer-categorized genes after 4 h MED23 depletion (BrU-seq) (A) or 4 h MED14 depletion (SLAM-seq) (B). (C) Kolmogorov-Smirnov D value, and D values of enhancer categories compared to no-enhancer genes after acute RAD21 or MED14 depletion. One-sided Kolmogorov-Smirnov test was performed; ∗∗∗ p < 0.001. (D) Effect of RAD21 depletion for long-range genes downregulated after MED14 depletion (log2FC <−0.3, FDR <0.05) compared to unaffected long-range genes. Two-sided Wilcoxon rank-sum test; ∗∗ p < 0.01. (E) Schematic and western blot validation of LDB1-FKBP degron lines in K562 EC100 cells, one representative clone. n = 2 clonal cell lines were used for all degron experiments. (F) FACS validation of EC100-GFP reporter after LDB1 depletion. (G) Cumulative distribution curves of log2FC of enhancer-categorized genes in BrU-seq, after 4 h LDB1 depletion. (H) Kolmogorov-Smirnov D values (one-sided test) after LDB1 depletion of enhancer genes versus no-enhancer genes. ∗ p < 0.05; ∗∗∗ p < 0.001. (I) LDB1 level on enhancers based on LDB1 ChIP-seq. (J) Effect of acute LDB1 depletion stratified for LDB1 level present at the enhancers. Quartiles were determined by ranking all enhancers defined in the three categories on LDB1 level, and then genes were assigned to be connected to either the LDB1 lowest (light purple) or highest (dark purple) 25% LDB1 bound at the enhancer. Two-sided Wilcoxon rank-sum test; ∗ p < 0.05; ∗∗ p < 0.01; ∗∗∗ p < 0.001. (K) Effect of RAD21 depletion for long-range genes downregulated after LDB1 depletion (log2FC < −0.3, FDR < 0.05) compared to unaffected long-range genes. Two-sided Wilcoxon rank-sum test; ∗∗∗ p < 0.001. See also Figures S5 and .

Article Snippet: To deplete MED23 and LDB1, dTAG-7 (TOCRIS, Cat#6912) was added to the medium in a final concentration of 500nM.

Techniques: Western Blot, Biomarker Discovery, ChIP-sequencing

Journal: Cell Genomics

Article Title: Long-range enhancer-controlled genes are hypersensitive to regulatory factor perturbations

doi: 10.1016/j.xgen.2025.100778

Figure Lengend Snippet: Summary of key results Cohesin regulates genes connected to enhancers in a distance-specific manner, being necessary for long-range activation but hindering short-range enhancer function. Mediator generally affects gene expression but displays a bias for long-range connected genes. This is also the case for other factors like LDB1, where this is due to long-range enhancers binding higher levels of such regulatory proteins.

Article Snippet: To deplete MED23 and LDB1, dTAG-7 (TOCRIS, Cat#6912) was added to the medium in a final concentration of 500nM.

Techniques: Activation Assay, Gene Expression, Binding Assay

Journal: Cell Genomics

Article Title: Long-range enhancer-controlled genes are hypersensitive to regulatory factor perturbations

doi: 10.1016/j.xgen.2025.100778

Figure Lengend Snippet:

Article Snippet: To deplete MED23 and LDB1, dTAG-7 (TOCRIS, Cat#6912) was added to the medium in a final concentration of 500nM.

Techniques: Virus, Recombinant, Isolation, Western Blot, Construct, Software, Sequencing, Flow Cytometry

Journal: Nature Communications

Article Title: Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions

doi: 10.1038/s41467-024-55403-7

Figure Lengend Snippet: a Frequency of Footprint-C 1D peak sites with 1, 2, 3, or 4+ footprints in K562 or HEK293T. b V-plots are shown for two 1 V sites with tracks from Footprint-C fragment ends, 1D signal, DNase-seq, CTCF and MAZ ChIP-seq. c V-plot is shown for one 3 V site with tracks from Footprint-C fragment ends, 1D signal, DNase-seq, TBP, CTCF and ZNF384 ChIP-seq. d Frequency of each TF with footprints in 1 V or 2 V+ sites in K562 or HEK293T. e Frequency of top 40 TF-TF pairs, from all 2 V sites in K562 or HEK293T. f , h Frequency of motif orientation of all CTCF:CTCF ( f ) or CTCF:FOX ( h ) pairs from 2 V sites in K562 or HEK293T. g , i Screenshots showing tracks from Footprint-C 1D, CTCF, RAD21, FOXK2 ChIP-seq and MNase-seq in K562. j V-plots of three types of CTCF 1 V sites are shown with CTCF and other TF ChIP-seq, and Footprint-C 1D average signal in K562. A diagram is shown at the bottom. The red arrows in b , c , g , i mark the indexed CTCF or FOX motifs.

Article Snippet: The RAD21 degron cells were treated with 1 μM dTAG-7 (MCE, HY-123941) or DMSO as control for 4 h.

Techniques: ChIP-sequencing

Journal: Nature Communications

Article Title: Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions

doi: 10.1038/s41467-024-55403-7

Figure Lengend Snippet: a Frequency of read mate orientation of different Hi-C datasets when distance <1 kb. b A screenshot showing Footprint-C contact heatmap with tracks from H3K27ac, ZNF143, KLF16, CTCF, RAD21 ChIP-seq, total RNA-seq, DNase-seq and Footprint-C 1D in K562. Gray shades mark the positions of non-CTCF loop anchors. c Number of loops (>20 kb) or stripes detected in Footprint-C, Micro-C, or in situ Hi-C datasets at different sampling size or by different methods. d Overlap of Mustache loops between Footprint-C & Micro-C datasets in K562. e Aggregate plots for common or Footprint-C specific loops. f Fraction of different loop types from common or Footprint-C specific loops. Enh, enhancer. Pro, promoter. g Size of common or Footprint-C specific structural A-A or B-B loops. Min: lower end of violin. Q1: lower bound of box. Q2: line in box. Q3: higher bound of box. Max: higher end of violin. P was calculated by two-sided Wilcoxon–Mann–Whitney test. Effect sizes are shown. h Footprint-C (right up) and Micro-C (left down) contact heatmaps at the same sampling size of 1800 M contacts showing one specific A-A (left) or B-B (right) structural loop, with tracks from genome annotation, PC1 value, CTCF, RAD21 or H3K9me3 ChIP-seq. Black squares mark the two loops. i , Aggregate plots of loops in DMSO or dTAG-7 treated HEK293T. The loops were from Footprint-C in WT HEK293T, and were aggregated at the center of a ±200 kb window at 5-kb resolution. The average enrichment score for loops was shown in top left corner. Source data are provided as a Source Data file.

Article Snippet: The RAD21 degron cells were treated with 1 μM dTAG-7 (MCE, HY-123941) or DMSO as control for 4 h.

Techniques: Hi-C, ChIP-sequencing, RNA Sequencing Assay, In Situ, Sampling, MANN-WHITNEY