Journal: bioRxiv

Article Title: An RNA binding module of SWI/SNF is required for activation of cell-type specific enhancers and super-enhancers in early development

doi: 10.1101/2022.09.06.506785

Figure Lengend Snippet: (A-B) Heatmaps of all H3K4me1 (green) peaks detected by CUT&RUN for wild type and AT hook deletion mutants in naïve (A) and primed (B) cells are shown. (C-D) The heatmaps shows the extent which MLL3/4 (red) and H3K4me1 (green) overlap in naïve (C) and primed (D) cells in cis-regulatory regions and their dependency on the AT-hook of BRG1. (E) Heatmaps of H3K4me1 (green), H3K27ac (red) and BRG1 (blue) are shown for those regions where BRG1 and H3K27ac co-localize in only naïve or primed cells.

Article Snippet: CUT&RUN for MLL3/4, BRG1, H3K27ac and H3K4me1 in E14 WT and mutant ES cells was done using CUTANA ChIC/CUT&RUN kit (Epicypher #14-1048) following manufacturer’s protocol.

Techniques:

Journal: bioRxiv

Article Title: An RNA binding module of SWI/SNF is required for activation of cell-type specific enhancers and super-enhancers in early development

doi: 10.1101/2022.09.06.506785

Figure Lengend Snippet: (A) Venn diagram shows naïve and primed specific intronic-intergenic ATAC-seq peak. (B) Heatmap showing SMARCA4 localization (blue), ATAC-signals (grey), and active enhancer histone marks (H3K27ac [red], and H3K4me1 [green]) at naïve (top) and primed (bottom) specific intronic-intergenic ATAC-seq peaks. ChIP-seq signals are sorted based on WT SMARCA4 in each condition. (C ) Heatmap showing ATAC signals in the two independent clones of the AT-hook mutant in naïve (top) and primed (bottom) states versus WT. ATAC signals are sorted based on WT. (D ) Heatmap shows the ATAC-signals for WT and dAT-mutants in naïve (top) and primed (bottom) conditions that are unaltered; N represents the number of intronic-intergenic ATAC-seq peaks in each category. (E) Heatmap showing the pluripotency and epiblast specific (EpiSC) specific transcription factors (TFs) motif enrichment between AT-hook dependent -vs.-AT-hook independent ATAC-seq intronic-intergenic peaks in naïve and primed states. (F) DNA footprinting shows loss of primed/EpiSC specific TF Zic3 (left panel) and pluripotency TFs O ct4- S ox2- T cf- N anog (right panel) binding in the AT-hook deletion mutants.

Article Snippet: CUT&RUN for MLL3/4, BRG1, H3K27ac and H3K4me1 in E14 WT and mutant ES cells was done using CUTANA ChIC/CUT&RUN kit (Epicypher #14-1048) following manufacturer’s protocol.

Techniques: ChIP-sequencing, Clone Assay, Mutagenesis, DNA Footprinting, Binding Assay

Journal: Cell reports

Article Title: Age-independent and targetable transcription factor networks regulating CD8 + T cell senescence in aging humans

doi: 10.1016/j.celrep.2025.116795

Figure Lengend Snippet: (A) Arc plot summarizing the evolution of the most prominent chromatin states in senescent CD8 + T cells. The edge width is proportional to the number of 200 bp bins undergoing the indicated chromatin state transition. (B) Genome-wide signal intensity heatmaps of H3K4me1, H3K27ac, ATAC-seq, and H3K27me3 at active enhancers (top) and unmarked chromatin (bottom) in SA-β-gal-low and SA-β-gal-high CD8 + T cells. The scale bars indicate the normalized signal. (C) Dot plot of the correspondence analysis linking chromatin state transitions to DEG modules from . Significance of the association was calculated using a chi-square test. (D) Genome browser snapshot of the TBKBP1 and TBX21 loci, showing signal tracks for RNA-seq, ATAC-seq, H3K4me1, H3K27ac, and H3K27me3 in SA-β-gal-low and SA-β-gal-high CD8 + T cells. (A–D) CUT&Tag data were generated from SA-β-gal-low and SA-β-gal-high CD8 + T cells from three younger donors. (E–G) Averaged heatmaps of color-coded modules (E and G) and PCA projection (F) of DEGs identified for the indicated comparisons (top of heatmaps and PCA plot). The scale bar (E and G) indicates the row Z score of the regularized log-transformed counts. (H) Functional overrepresentation analysis map showing significant associations of the MSigDB hallmark gene sets for the indicated DEG modules from (G). (I) Upset plot showing the unique and shared DARs for the indicated CD8 + T cell states. (J and K) As in (E) and (G) for the identified DARs of the indicated comparisons. Data for naive and stimulated CD8 + T cells are from GEO: GSE212347 .

Article Snippet: We performed CUT&Tag on 75,000–100,000 sorted CD8 + fSA-βGal low and high from young donors ( n = 3) with the CUTANA CUT&Tag kit (Epicypher) using the following antibodies: H3K4me1 (Epicypher: 13–0057), H3K27me3 (Epicypher: 13–005), H3K27ac (Active Motif: 39,133) and rabbit IgG as a negative control (Epicypher: 13–0042), according to the manufacturer’s instructions.

Techniques: Genome Wide, RNA Sequencing, Generated, Transformation Assay, Functional Assay

Journal: Molecular cell

Article Title: Examining the roles of H3K4 methylation states with systematically characterized antibodies

doi: 10.1016/j.molcel.2018.08.015

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Anti-H3K4me1 antibody EpiGentek A-4031-050, Lot Number 606359. , EpiGentek , Cat#A-4031–050.

Techniques: Virus, Recombinant, Synthesized, Peptide Microarray, Software