Fig 1: PTFs and Jun co-occupy active enhancers and promoters associated with Yap independency.a Cut&Tag signal heatmaps from the indicated antibodies within ±3kb from the centers of merged CRE and TSS sites bound by at least one of the TFs or histones in #5462 cells. TSS sites are defined by H3K4me3 positivity. b Relative Tag Density from Cut&Tag analysis of #5462 cells with indicated antibodies at ±250 bp from the centers of the indicated HOMER motif sites. c Summary of the numbers of active (light red) and inactive (light green) CRE and TSS sites with different binding statuses by Jun, Sox2, Sox5, and/or Twist2 in #5462 cells. Active CRE and TSS are defined by H3K27ac and BRD4 double positivity. Sox5|Twist2+ indicates peaks bound by either Sox5 or Twist2, but not both. d Aggregated Jun, Twist2, Sox2, and Sox5 Cut&Tag signals within ±2 kb from the centers of BRD4 peaks associated with YapDH or YapDL in #5462 cells. e Summary of the numbers of genomic loci associated with YapDH (black) and YapDL (red) with different binding statuses by Jun, Sox2, Sox5, and Twist2 in #5462 cells. f Genomic tracks showing the distributions of Cut&Tag peaks from indicated antibodies surrounding the Jun gene in #5462 cells. g Summary of the percentages of Yap peaks with different binding statuses by Jun, Sox2, Sox5, and Twist2 in #5462 cells. Source data are provided within a Source Data file. Cut&Tag data are deposited in the GEO database under accession code GSE224566.
Fig 2: PTFs and Jun form a CRC with Jun acting as the dominant chromatin anchor in Yap-independent PDAC cells.a Schematic illustration showing chromatin-bound TF (green) recognized by its antibody (gray), which in turn recruits ProteinA-Tn5 (PrA-Tn5: dark blue) to tagment the accessible chromatin regions in the vicinity. The motif (red) bound by the TF is protected from tagmentation, leaving a footprint (FP) whose relative depth is calculated by dividing the absolute FP Depth by Flank Height (the height of peak signals immediately flanking the motif over the background). Created by S.M. b Scatter plot representing Relative FP Depths and the corresponding Aggregated Flank Heights of the indicated TFs at the sites matching the indicated motifs. TFs are represented by shapes (Jun: circle; Sox2: square; Sox5: triangle; Twist2: diamond). JASPAR motifs are presented by line colors (Jun_MA0489.2: red; SOX2_MA0143.4: purple; Sox5_MA0087.2: blue; TWIST1_MA1123.2: orange). c Aggregated signals from bound (red), unbound (blue), or all (gray) Jun, Sox2, Sox5, and Twist2 peaks centered on the indicated motif (marked by gray dashed lines). The total numbers of bound, unbound and all peaks for each antibody are Jun: 2785, 7731, and 10516; Sox2: 553, 2279, and 2832; Sox5: 127, 1452, and 1579, and Twist2: 230, 1078, and 1308. d Aggregated signal centering the Jun_MA0489.2 motif (marked by gray dashed lines) within the active (pink) or inactive (green) CRE sites bound by Jun, Sox2, Sox5, or Twist2. e Western blot analysis of indicated proteins in #5462 cells carrying Dox-inducible shRNAs or sgRNAs targeting indicated PTFs or constitutively overexpressing a dominant negative Jun mutant (JunDN) in the presence or absence of Dox. Vinc was used as the loading control. Shown is representative of three independent experiments. f A working model of cooperative binding of Jun and PTFs to AP-1 sites that drive active transcription of target genes. Created with BioRender.com. Source data are provided within a Source Data file. Cut&Tag data are deposited in the GEO database under accession code GSE224566.
Supplier Page from DNASU for TWIST2 (Homo sapiens) in pLenti6.2/V5-DEST (V5-tagged lentiviral mammalian expression vector)