Extended Data Fig. 6: Hypomethylation of SMRs guides SWI/SNF complex binding.
a, Volcano plot showing DEGs between ILCs and ILCP2s. Statistical analyses were performed using two-tailed unpaired Student’s t test. The blue dots represent genes which were downregulated in ILCs compared with ILCP2s (log2(fold change) < -0.4, P < 0.05). The red dots represent genes which were upregulated in ILCs compared with ILCP2s (log2(fold change) > 0.4, P < 0.05). b, Boxplots showing Smarcc1 (coding BAF155) expression levels in ILCP1s, ILCP2s and ILCP2s in differentiation stages. UHRF1-mCherry+ ILCP (ILCP1s) and UHRF1-mCherry− ILCPs (ILCP2s) were isolated and ILCP2s were cultured with OP9-DL1 cells in media with 25 ng/ml IL-7 and 25 ng/ml SCF for the indicated days in vitro. The expression levels of Smarcc1 gene were analyzed by qPCR and shown. Each box represents the median and the 25% and 75% quartiles, and the whiskers indicate 1.5 times the interquartile range. Statistical analyses were performed using one-way ANOVA. (n = 3 cultures per group). c, Bar graph showing BAF155 occupancy at SMRs in ILCPs assessed by CUT&Tag-qPCR. ILCPs were transduced with dC-DNMT1 or catalytically inactive dC-dDNMT1, and enrichment of BAF155 was quantified. Data are presented as mean ± s.d. Statistical analyses were performed using two-tailed unpaired Student’s t-test. (n = 3 cultures per group). d, ATAC-seq analysis showing chromatin accessibility of SMRs in ILCPs transduced with dC-DNMT1 or dC-dDNMT1 and SMR-targeting gRNAs after 7 days in vitro. e, Boxplots showing the expression levels of Tbx21, Bcl11b, and Rorc genes in ILCPs transduced with dC-DNMT1 or dC-dDNMT1 and SMR-targeting gRNAs at day 7 of culture of ILCPs. Each box represents the median and the 25% and 75% quartiles, and the whiskers indicate 1.5 times the interquartile range. Statistical analyses were performed using two-tailed unpaired Student’s t test. (n = 3 cultures per group). Data are representative of at least two (a, d) or three (b-c, e) independent experiments.
