Fig. 5 | Nature Communications

Fig. 5

From: A non-canonical BRD9-containing BAF chromatin remodeling complex regulates naive pluripotency in mouse embryonic stem cells

Fig. 5

GBAF complexes regulate naive pluripotency. a Bar graph of mean mRNA expression FC for the pluripotency TFs upon either I-BRD9 treatment of v6.5 ESCs or tamoxifen treatment of Arid1af/fCreERT2 ESCs (ARID1A KO) over DMSO or ethanol, respectively, from two biological replicates. 1.5-FC decrease is denoted with a dotted line. Error bar = standard deviation. Benjamin-Hochberg FDR < 0.05 is denoted with triple asterisks. b Brightfield images of ESCs treated with either DMSO or I-BRD9 at 3 or 10 µM for 6 days. Scale bar = 150 µm. c Quantification of ESC colonies cultured with the indicated treatment for 6 days. This is representative of two independent experiments. d Representative images of wells containing ESCs treated with the indicated vehicle or BRD9i for 6 days then assayed for alkaline phosphatase (AP) activity. e Quantification of the colonies in d, showing the mean and standard deviation of two biological replicates. Error bars = standard deviation. Source data are provided as Source Data file. f Venn diagram overlap of DEGs with I-BRD9 treatment for 48 h and DEGs with FGF/Activin A addition over serum/LIF (EpiESC/ESC). p value was calculated using hypergeometric test of overlap, with population size being the total number of genes tested (N = 24,538). g Scatterplot of the mRNA log2 FCs in I-BRD9/DMSO and EpiESC/ESC for the 477 common DEGs in f. Linear regression analysis was performed to calculate the R2. Best fit is represented as a pink dashed line. h As in g, but of the mRNA log2 FC of DEGs that are common between Arid1af/fCreERT2 ESCs treated with tamoxifen/ethanol and EpiESC/ESC (n = 302). Best fit is represented as a gray dashed line. i Significance of TF binding on the 477 common DEGs in f. p values were calculated using hypergeometric test. In parentheses are the percentages of EpiESC genes that are bound by the corresponding TFs. j Heat map of mRNA log2 FCs for the indicated genes in EpiESC/ESC, I-BRD9/DMSO, and Arid1af/fCreERT2 ESCs tamoxifen/ethanol

Source data

Back to article page