Journal: bioRxiv

Article Title: FACT depletion results in a temporal cascade of chromatin disruption preceding transcriptional collapse in stem cells

doi: 10.64898/2026.02.26.708215

Figure Lengend Snippet: (A) Schematic of experimental design for nascent transcription analysis. SPT16-dTAG ES cells were treated with dTAG-13 or vehicle control (−; DMSO) for indicated times, followed by pulse labeling with 4-thiouridine (4sU) to capture newly transcribed RNA for TT-seq analysis. (B) Volcano plot showing differential nascent transcription at 10 min of SPT16 depletion compared to vehicle control. X-axis shows log ₂ fold change; y-axis shows −log ₁₀ FDR. Significantly upregulated genes (red, FDR<0.05 and Log 2 FC>1) and downregulated genes (blue, FDR<0.05 and Log 2 FC<1) are highlighted. (C) Volcano plot as in (B) showing differential nascent transcription at 30 min of SPT16 depletion compared to vehicle control. (D) Volcano plot as in (B) showing differential nascent transcription at 2 h of SPT16 depletion compared to vehicle control. (E) Model summarizing the temporal sequence of events following FACT depletion. FACT loss causes H3K4me3 and nucleosome loss at 5’ ends of genes. TFs are mislocalized to gene bodies, RNAPII accumulates over 5’ ends of genes resulting in eventual downregulation of transcription. See also Figure S7.

Article Snippet: Following protein depletion, cells were treated with 2i LIF media containing 500 μM 4-thiouridine (4sU; Carbosynth T4509) dissolved in 100% DMSO and incubated at 37°C and 5% CO 2 for 5 min to label nascent transcripts.

Techniques: Control, Labeling, Sequencing

Journal: bioRxiv

Article Title: FACT depletion results in a temporal cascade of chromatin disruption preceding transcriptional collapse in stem cells

doi: 10.64898/2026.02.26.708215

Figure Lengend Snippet: (A) Schematic of experimental design for nascent transcription analysis. SPT16-dTAG ES cells were treated with dTAG-13 or vehicle control (−; DMSO) for indicated times, followed by pulse labeling with 4-thiouridine (4sU) to capture newly transcribed RNA for TT-seq analysis. (B) Volcano plot showing differential nascent transcription at 10 min of SPT16 depletion compared to vehicle control. X-axis shows log ₂ fold change; y-axis shows −log ₁₀ FDR. Significantly upregulated genes (red, FDR<0.05 and Log 2 FC>1) and downregulated genes (blue, FDR<0.05 and Log 2 FC<1) are highlighted. (C) Volcano plot as in (B) showing differential nascent transcription at 30 min of SPT16 depletion compared to vehicle control. (D) Volcano plot as in (B) showing differential nascent transcription at 2 h of SPT16 depletion compared to vehicle control. (E) Model summarizing the temporal sequence of events following FACT depletion. FACT loss causes H3K4me3 and nucleosome loss at 5’ ends of genes. TFs are mislocalized to gene bodies, RNAPII accumulates over 5’ ends of genes resulting in eventual downregulation of transcription. See also Figure S7.

Article Snippet: Following protein depletion, cells were treated with 2i LIF media containing 500 μM 4-thiouridine (4sU; Carbosynth T4509) dissolved in 100% DMSO and incubated at 37°C and 5% CO 2 for 5 min to label nascent transcripts.

Techniques: Control, Labeling, Sequencing