triptolide  (Thermo Fisher)

Journal: bioRxiv

Article Title: Histone H4 acetyl-methyllysine marks accessible chromatin that resists compaction

doi: 10.64898/2026.04.17.718779

Figure Lengend Snippet: ( A ) Relative promoter accessibility (±50 bp of the TSS) in HEK293T cells as determined by ATAC-seq. Normalized ATAC-seq signal was binned by promoter Kacme levels (±1 kb of the TSS) as determined by ChIP-seq. ( B ) Genome browser visualization of ATAC-seq and Kacme ChIP-seq profiles at selected loci on chromosome 19 in HEK293T cells. ( C ) Heatmaps of Kacme ChIP-seq and H3K27me3 CUT&RUN signal centered on transcription start sites (±2.5 kb) across all annotated HEK293T promoter regions. ( D ) Relative promoter accessibility in HEK293T cells for genes in the 25 th or 75 th percentiles of Kacme CUT&RUN levels. Data are binned by H4K5ac CUT&RUN signal. ( E ) Left: Representative western blot of histones from HEK293T cells treated with the transcription inhibitors triptolide (10 μM, 1 h) or flavopiridol (500 nM, 1 h). Right: Venn diagram showing the overlap between genes with a promoter-proximal Kacme peak (±3 kb of the TSS) in untreated HEK293T cells (light blue) and in triptolide-treated HEK293T cells (light red). Kacme peaks were identified using MACS2. ( F ) Genome browser tracks showing ATAC-seq, Kacme, H3K4me1, H3K27ac, and H3K4me3 signal profiles across an enhancer-rich locus in HEK293T cells. ( G ) Heatmaps and aggregated signal profiles for ATAC-seq, Kacme, H3K27ac, H3K4me1, and H3K27me3 across six enhancer clusters identified in HEK293T cells by k-means clustering. Aggregated profiles show the mean signal across enhancer regions within each cluster. ( H ) HOMER known motif analysis for enhancer clusters 1 and 2 , showing the top 20 enriched motifs with their best-match transcription factors and associated p-values. FOX proteins highlighted in magenta, CTCF highlighted in green. ( A, D ) Distribution means compared with two-tailed unpaired Wilcoxon test for two biological replicates. *** = p < 0.001.

Article Snippet: For transcriptional inhibition studies, HEK293T cells were treated with 10 μM triptolide (MCE, HY-32735) or 500 nM flavopiridol (Sigma Aldrich, F3055) for 1hr.

Techniques: ChIP-sequencing, Western Blot, Two Tailed Test

Journal: bioRxiv

Article Title: Histone H4 acetyl-methyllysine marks accessible chromatin that resists compaction

doi: 10.64898/2026.04.17.718779

Figure Lengend Snippet: ( A ) Relative promoter accessibility in THP-1 cells for genes in the 25 th or 75 th percentiles of Kacme ChIP-seq levels. Data are binned by H4K5ac ChIP-seq signal. ( B ) Relative promoter accessibility in THP-1 cells for genes in the 25 th or 75 th percentiles of Kacme ChIP-seq levels. Data are binned by H3K27ac ChIP-seq signal. ( C ) Genome browser visualization of Kacme ChIP-seq (untreated) and Kacme CUT&RUN (triptolide-treated) profiles at representative loci on chromosome 5 in HEK293T cells. ( B-C ) Distribution means compared with two-tailed unpaired Wilcoxon test for two biological replicates. *** = p < 0.001; * = p < 0.05; NS = Not Significant.

Article Snippet: For transcriptional inhibition studies, HEK293T cells were treated with 10 μM triptolide (MCE, HY-32735) or 500 nM flavopiridol (Sigma Aldrich, F3055) for 1hr.

Techniques: ChIP-sequencing, Two Tailed Test

Journal: Nucleic Acids Research

Article Title: Multiplexed TrAEL-seq captures DNA replication dynamics in mammalian cells

doi: 10.1093/nar/gkag212

Figure Lengend Snippet: Causes of replication fork processivity differences across the genome. ( A ) Metaplot of TrAEL-seq read count in DLD-1 cells averaged across genes ± 100 kb. Genes are stratified for transcriptional activity based on PRO-seq into 0%–40%, 40–70%, 70%–90%, and 90%–100% categories. Profiles were normalized individually to make background read counts as close as possible. ( B ) Plots of total TrAEL-seq read count at increasing distance from replication Initiation Zones, stratified for nascent transcription level by PRO-seq. Analysis was performed as in Fig. , but the genomic windows included were filtered to remove the top 25%, 50%, or 75% of regions based on PRO-seq read count. ( C ) Total TrAEL-seq read count at increasing distance from replication Initiation Zones in untreated DLD-1 cells or cells treated for 2 h with 100 µM DRB or for 4 h with 3 µM triptolide. ( D ) Metaplot of TrAEL-seq read count over genes ± 100 kb as in panel (A) in DLD-1 cells ± DRB and triptolide (datasets as in panel (C), data is an average of the two biological replicates shown). ( E ) Total TrAEL-seq read count at increasing distance from replication Initiation Zones in untreated DLD-1 cells and cells treated for with 1 µM Cerelasertib for 24 h. ( F ) Total TrAEL-seq read count at increasing distance from replication Initiation Zones in untreated PC9 cells and cells treated for 24 h with 16 nM palbociclib.

Article Snippet: Hydroxyurea (Merck H78627 ) was used at 20–100 μM for 2 h, Ceralasertib (Merck TA9H11E41972) at 1 μM for 24 h, palbociclib (Thermo Fisher Scientific 16430568) at 16 nM for 24 h, triptolide (Thermo Fisher Scientific PG490) at 3 μM for 4 h.

Techniques: Activity Assay