Journal: bioRxiv

Article Title: Decoding the cell intrinsic and extrinsic roles of PRC2 in early embryogenesis

doi: 10.64898/2026.01.20.700679

Figure Lengend Snippet: ( a ) Scatter plots showing the reproducibility between biological replicates for E4.5 ICM RNA-seq datasets. Pearson correlation coefficients are shown. ( b ) Bar plots showing the expression changes of representative pluripotent markers in DMSO and dTAG groups of E4.5 ICM cells. ( c ) Scatter plots showing the reproducibility between biological replicates for H3K27me3 CUT&RUN datasets. Pearson correlation coefficient is shown. ( d ) Heatmap illustrating RNA and H3K27me3 levels for the differentially expressed genes in E4.5 ICM cells. Housekeeping (HK) genes serve as negative controls for H3K27me3. ( e ) Scatter plots showing the reproducibility between biological replicates for E4.5 ICM H2Aub CUT&RUN datasets. Pearson correlation coefficients are shown. ( f ) Heatmap showing genome-wide 10 kb bins of signals for H2Aub, H3K4me3 and ATAC-seq peaks in E4.5 ICM with or without EED degradation. All the bins were classified into two subgroups based on the level of H3K27me3. C: peak center.

Article Snippet: Primary antibodies anti-H3K4me3 (1:100, CST, 9727S), anti-H3K27me3 (1:100, Diagenode, C15410069), anti-H2AK119ub1 (1:100, CST, 8240S), and anti-ESRRB (1:100, Proteintech, 22644-1-AP) were used for CUT&RUN.

Techniques: RNA Sequencing, Expressing, Genome Wide

Journal: bioRxiv

Article Title: Decoding the cell intrinsic and extrinsic roles of PRC2 in early embryogenesis

doi: 10.64898/2026.01.20.700679

Figure Lengend Snippet: ( a-b ) Immunostaining images showing the rapid depletion of EED in ex vivo cultured E6.5 ( a ) and E7.5 ( b ) post-implantation embryos following 4 hr treatment with dTAG V -1. Hoechst 33342. Scale bar, 100 μm. ( c ) Scatter plots showing the reproducibility between biological replicates for E6.5 EPI, ExE, and VE RNA-seq datasets. Pearson correlation coefficients are shown. ( d ) Scatter plot comparing gene expression changes between DMSO and dTAG groups in E6.5 EPI and VE. Red and blue dots represent up- and down-regulated repeat subfamilies in the dTAG group, respectively. The cutoff used to define differentially expressed repeats: fold change (FC) >= 2, adjusted p -value < 0.05 and FPKM >= 1. ( e ) Scatter plot showing the number of bivalent genes (red dots) in E6.5 ExE. ( f ) Boxplot showing the E6.5 ExE bivalent gene expressions changes between DMSO and dTAG groups. In the boxplot, the central band represents the median. The lower and upper edges of the box represent the first and third quartiles, respectively. The whiskers of the boxplot extend to 1.5 times interquartile range (IQR). P -values were calculated with two-sided Wilcoxon signed rank test. ( g ) GO term analyses for the up-regulated genes in E6.5 ExE upon EED depletion. ( h ) Scatter plots showing the reproducibility between biological replicates for H3K27me3 CUT&RUN datasets. Pearson correlation coefficients are shown.

Article Snippet: Primary antibodies anti-H3K4me3 (1:100, CST, 9727S), anti-H3K27me3 (1:100, Diagenode, C15410069), anti-H2AK119ub1 (1:100, CST, 8240S), and anti-ESRRB (1:100, Proteintech, 22644-1-AP) were used for CUT&RUN.

Techniques: Immunostaining, Ex Vivo, Cell Culture, RNA Sequencing, Gene Expression

Journal: bioRxiv

Article Title: Decoding the cell intrinsic and extrinsic roles of PRC2 in early embryogenesis

doi: 10.64898/2026.01.20.700679

Figure Lengend Snippet: ( a ) Heatmap illustrating ESRRB CUT&RUN signals in E6.5 and E7.0 ExE. Two biological replicates for each stage are shown. ( b ) Genome browser views of ESRRB binding and RNA signals at the indicated genomic loci. ( c ) Heatmap showing the H3K27ac changes caused by Esrrb KO at ESRRB-bound promoters, introns, and distal regions in E6.5 ExE. ( d ) Genome browser views of ESRRB binding and H3K27ac changes at the indicated genomic loci. ( e ) Left panel: heatmaps showing ATAC signal and the H3K27ac changes caused by Esrrb KO at ESRRB and TFAP2C co-bound regions. The peaks were classified into three clusters based on ESRRB and TFAP2C enrichment levels. ( f ) Genome browser views of ESRRB and TFAP2C binding, ATAC signal, and H3K27ac level at the indicated genomic loci. ( g ) Diagram summarizing the EED-ESRRB-BMP4 axis in regulating PGC specification during gastrulation. ( h ) Diagram illustrating that ESRRB regulates its target genes by activating enhancers.

Article Snippet: Primary antibodies anti-H3K4me3 (1:100, CST, 9727S), anti-H3K27me3 (1:100, Diagenode, C15410069), anti-H2AK119ub1 (1:100, CST, 8240S), and anti-ESRRB (1:100, Proteintech, 22644-1-AP) were used for CUT&RUN.

Techniques: Binding Assay

Journal: bioRxiv

Article Title: Decoding the cell intrinsic and extrinsic roles of PRC2 in early embryogenesis

doi: 10.64898/2026.01.20.700679

Figure Lengend Snippet: ( a ) Scatter plots showing the reproducibility between biological replicates for E6.5 and E7.0 ExE ESRRB CUT&RUN datasets. Pearson correlation coefficients are shown. ( b ) Heatmap showing the ESRRB and SOX2 binding at E6.5 ExE lienage. C: peak centers. ( c ) Examples of ExE developmental genes with both ESRRB and SOX2 binding (shaded) at E6.5 ExE lineage. ( d ) Pie chart showing the ESRRB peaks distributions in E6.5 and E7.0 ExE. ( e ) Genome browser views of ESRRB and H3K27ac signals (shaded) in E6.5 ExE of WT and Esrrb KO embryos.

Article Snippet: Primary antibodies anti-H3K4me3 (1:100, CST, 9727S), anti-H3K27me3 (1:100, Diagenode, C15410069), anti-H2AK119ub1 (1:100, CST, 8240S), and anti-ESRRB (1:100, Proteintech, 22644-1-AP) were used for CUT&RUN.

Techniques: Binding Assay

Journal: Gene Regulation and Systems Biology

Article Title: Alpha-Tocopherol Modulates Transcriptional Activities that Affect Essential Biological Processes in Bovine Cells

doi: 10.4137/GRSB.S6007

Figure Lengend Snippet: α-tocopheryl modulates biological networks generated using transcription regulation algorithm.

Article Snippet: Rabbit anti-ESR1 antibody (OriGene, Rockville, MD, Cat. No. TA300376), Mouse monoclonal IgG activated C3 antibody (Santa Cruz Biotech, Santa Cruz, CA, Cat. No. sc-55458) and rabbit anti-Erk1/Erk2 (extracellular signal-regulated kinases or mitogen-activated protein kinase being 3) antibody (Calbiochem, San Diego, Cat. No. 442704) were used for Western Blots.

Techniques: Generated, Gene Expression

Journal: Gene Regulation and Systems Biology

Article Title: Alpha-Tocopherol Modulates Transcriptional Activities that Affect Essential Biological Processes in Bovine Cells

doi: 10.4137/GRSB.S6007

Figure Lengend Snippet: Representative biological network generated using the Analyze Networks Transcription regulation Algorithm. Up-regulated genes are marked with red circles and down-regulated genes are marked with blue circles. The network is centered with NF-κB and ESR1. All other transcription factors are shown in the left panel. All the symbols in the network are listed in .

Article Snippet: Rabbit anti-ESR1 antibody (OriGene, Rockville, MD, Cat. No. TA300376), Mouse monoclonal IgG activated C3 antibody (Santa Cruz Biotech, Santa Cruz, CA, Cat. No. sc-55458) and rabbit anti-Erk1/Erk2 (extracellular signal-regulated kinases or mitogen-activated protein kinase being 3) antibody (Calbiochem, San Diego, Cat. No. 442704) were used for Western Blots.

Techniques: Generated

Journal: Gene Regulation and Systems Biology

Article Title: Alpha-Tocopherol Modulates Transcriptional Activities that Affect Essential Biological Processes in Bovine Cells

doi: 10.4137/GRSB.S6007

Figure Lengend Snippet: The representative network of the most relevant biological networks that is unique to up-regulated networks using the Analyze Networks Transcription regulation Algorithm. This is a variant of the shortest paths algorithm with relative enrichment and relative saturation of networks with canonical pathways. Key network objects include ESR1, C3, Erk1/2 (shown in blue rectangles). Large orange rectangle highlights the transcription factors.

Article Snippet: Rabbit anti-ESR1 antibody (OriGene, Rockville, MD, Cat. No. TA300376), Mouse monoclonal IgG activated C3 antibody (Santa Cruz Biotech, Santa Cruz, CA, Cat. No. sc-55458) and rabbit anti-Erk1/Erk2 (extracellular signal-regulated kinases or mitogen-activated protein kinase being 3) antibody (Calbiochem, San Diego, Cat. No. 442704) were used for Western Blots.

Techniques: Variant Assay