Fig. 2

Transcriptome profiling of proliferating cells reveals a drop of α-defensin levels in Tcf7l2-deficient intestinal epithelium. A Single-cell transcriptome analysis of intestinal epithelial cells in Tcf7l2^wt/wt/Mki67^RFP/RFP/Villin-CreER^T2 (Tcf7l2^wt/wt) mice. Proliferating (i.e., Mki67-RFP-positive) epithelial cells were isolated and analyzed. The diagram on the left shows an UMAP (Uniform Manifold Approximation and Projection) visualization in which the cells are color-coded according to their identified cell type. For the full list of genes expressed in each cluster, see Additional file 2: Supplementary Table S2. The UMAP diagram on the top right side is colored based on the cell cycle phase. The right bottom UMAP diagram is an overlay of the UMAP clusters with arrows representing the lineage relationships between the cell types (RNA velocity). The violin diagram on the right shows the differential expression of key lineage markers in the identified clusters; the level of gene expression is indicated on the y-axis. Alpi, alkaline phosphatase, intestinal; Atoh1, atonal bHLH transcription factor 1; Defa5, defensin alpha 5; Fabp1, fatty acid binding protein 1; Lgr5, leucine-rich repeat-containing G protein-coupled receptor 5; Mki67, proliferation marker Ki-67; Neurog3, neurogenin 3; Olfm4, olfactomedin 4; Reg4, regenerating family member 4; Spdef, SAM pointed domain containing ETS transcription factor. B The bulk RNA sequencing heatmap shows differentially expressed antimicrobial/anti-inflammatory genes with color scaling indicating the expression level in Tcf7l2^wt/wt mice compared to the Tcf7l2^flox/flox tissue. Jejunum of the mice was analyzed 7 days after tamoxifen administration. Significant genes (adjusted p-value < 0.05 and |fold change (FC)|≥ 2) are shown. A complete list of differentially expressed genes can be found in Additional file 3: Supplementary Table S3. Hbegf, heparin binding EGF like growth factor; Pck1, phosphoenolpyruvate carboxykinase 1; Rasgef1b, RasGEF domain family member 1b