Journal: Communications Biology

Article Title: Sirt6 -mediated epigenetic modification of DNA accessibility is essential for Pou2f3 -induced thymic tuft cell development

doi: 10.1038/s42003-022-03484-9

Figure Lengend Snippet: a Heatmap of differentially accessible genes between Late Aire 2 cells and thymic tuft cells in scATAC-seq. The color scale indicates the level of gene activity. b UMAP visualization of the gene expression of Pou2f3 in scRNA-seq. c UMAP visualization of the motif accessibility score of Pou2f3 in scATAC-seq. d Gene expression of Pou2f3 in Pou2f3 + mTEC subsets in scATAC-seq was compared in a boxplot. Pou2f3 + mTEC II: n = 499, Pou2f3 + Late Aire 2 cells: n = 210, Pou2f3 + thymic tuft cells: n = 297. e Motif accessibility score of Pou2f3 in Pou2f3 + mTEC subsets in scATAC-seq was compared in a boxplot. Boxplots show the fragments at the promoter region ( f ) and TSS enrichment score ( g ) for Late Aire 2 cells (pink) and thymic tuft cells (blue). Late Aire 2 cells: n = 551, thymic tuft cells: n = 495. h Taste pathway-related gene (blue), Pou2f3 directly regulated gene sets (green), and tuft gene sets of scRNA-seq (orange) are calculated in a Venn diagram. The overlapping genes among them are shown on the right. The chromatin accessibility peaks of overlapping genes ( i ) and tuft-associated genes ( j ) are shown in scATAC-seq tracks. The arrow indicates the length and direction of the genes detected by scATAC-seq. The statistics was determined using Wilcoxon signed-rank test. **** p < 0.001.

Article Snippet: The primary antibody, anti-POU2F3 (Prosci, 7795), was diluted with Antibody Diluent II at 1:40, while the anti-rabbit secondary HRP antibody (042-206; ProteinSimple) was used directly.

Techniques: Activity Assay, Expressing

Journal: Communications Biology

Article Title: Sirt6 -mediated epigenetic modification of DNA accessibility is essential for Pou2f3 -induced thymic tuft cell development

doi: 10.1038/s42003-022-03484-9

Figure Lengend Snippet: a , b scATAC-seq data of WT and Sirt6 -deficient mTECs are coembedded into a single UMAP visualization ( a ) and are displayed separately ( b ). Cells are stained with the mTEC subset defined before. c Relative proportion of mTEC clusters between WT and Sirt6 cKO mice. d Simple Western analysis of POU2F3 expression in sorted mTECs (CD45 − EpCAM + UEA-1 + Ly51 − ) from 4-week-old WT and Sirt6 cKO mice. e UMAP visualization of the gene expression of Pou2f3 in WT (left) and Sirt6 cKO (right) scATAC-seq. The red scale in the UMAP plot indicates the level of Pou2f3 gene activity in scATAC-seq f UMAP visualization of the motif accessibility score of Pou2f3 in WT (left) and Sirt6 cKO (right) scATAC-seq. The blue scale in the UMAP plot indicates the level of Pou2f3 motif accessibility in scATAC-seq analyzed by chromVAR. g , h Motif accessibility scores of Klf3 ( g ) and Pou2f3 ( h ) in Late Aire 2 cells and thymic tuft cells of WT (Orange) and Sirt6 cKO mice (green) were compared in a violin plot. WT Late Aire 2 cells: n = 272, Sirt6 cKO Late Aire 2 cells: n = 500, WT thymic tuft cells: n = 501, Sirt6 cKO thymic tuft cells: n = 150. i , j Chromatin accessibility peaks of overlapping genes ( i ) and tuft-associated genes ( j ) mentioned in Fig. in WT and Sirt6 -deficient thymic tuft cells are shown in aggregated scATAC-seq tracks. The arrow indicates the length and direction of the genes detected by scATAC-seq. The statistics was determined using Wilcoxon signed-rank test. * p < 0.05, ** p < 0.01, *** p < 0.005 and **** p < 0.001.

Article Snippet: The primary antibody, anti-POU2F3 (Prosci, 7795), was diluted with Antibody Diluent II at 1:40, while the anti-rabbit secondary HRP antibody (042-206; ProteinSimple) was used directly.

Techniques: Staining, Western Blot, Expressing, Activity Assay