Fig. 3: aKG-dependent methylome regulates PC renewal in vivo.
From: Old mitochondria regulate niche renewal via α-ketoglutarate metabolism in stem cells
a, Impact of in vivo dm-aKG on 5hmC in intestinal cells along the crypt–villus axis. Representative image of a control mouse indicating high 5hmC in PCs (arrow). DAPI, blue; 5hmC, yellow; E-cadherin, grey. dm-aKG treatment increased nuclear 5hmC significantly in ISCs. A two-tailed, unpaired Student’s t-test (n = 4) was used. Data are shown as the mean ± s.d. b, Impact of in vivo dm-aKG on PC renewal. Cells that renewed within a week are EdU+ (arrowhead); pre-existing cells older than a week are EdU− (arrow). dm-aKG promoted PC renewal in all sections of the small intestine (D, duodenum; J, jejunum; I, ileum). A two-tailed, unpaired Student’s t-test (n = 4) was used. Data are shown as the mean ± s.d. Representative image of control crypt (blue, DAPI; red, lysozyme; yellow, EdU; white, E-cadherin). c, Volcano plot of transcriptomic changes in ISCs after 5 days of dm-aKG treatment (the blue data points are significant; false discovery rate (FDR) < 0.05, log2(fold change) > 1) d, Five representative hits of oxidative whole-genome bisulfite sequencing (WGBS-seq) differentially methylated or hydroxymethylated regions associated with PC or ISC function between ISCsmito-O (red track) and ISCsmito-Y (green track). e, dm-aKG induced more gains than losses of DhMRs in ISCs, as seen using E5hmC-seq. The bar graph shows the DhMR count for the indicated interval of hydroxymethylation difference. f, dm-aKG induced increased hydroxymethylation of WGBS-seq PC-associated and ISC-associated hits (Fto, Gata4 and Fut2), as seen with the E5hmC-seq control (yellow track) and dm-aKG-treated ISCs (teal track). TSS, transcription start site. Scale bar, 5 µm (a,b).
