Fig. 7: Extrinsic signals promote the transcriptional and epigenetic maturation of astrocytes.

a Experimental design to assess the effects of extrinsic signals on astrocyte maturation. Initial differentiation with BMP4 is followed by 7 days in different maturation conditions: control (basal medium in conventional two-dimensional cultures) ±FGF2 (control/FGF) or in three-dimensional gel-embedded cultures (3D/3D_FGF). b, c Expression of mature astrocyte-specific transcription factors (b) and other genes (c) in cultured astrocytes and cortical astrocytes (at postnatal day 4 (Astr_P4), and 2 months of age (Astr_2m)). Heatmaps of selected genes. Barplot showing that subsets of mature genes with low expression in control cultures are induced in other culture conditions. d ATAC-Seq genome tracks showing chromatin accessibility peaks around the TSS of the mature astrocyte-specific gene Slc1a2, which is expressed at higher levels in astrocytes in 3D cultures in the presence of FGF2 than in astrocytes in control cultures (see (c)). e Heatmaps showing global chromatin accessibility around ATAC peaks that are induced during maturation of cortical astrocytes and in astrocytes in 3D cultures with FGF2, but are absent in control cultures (5499 peaks). Statistical analysis and data presentation: Differential genes/peaks: DESeq2 analysis, each n = 3 (n = 4 for Astr_2m); two-sided Wald test with Benjamini–Hochberg correction; significance threshold: adjusted p-value ≤ 0.05, absolute log2(fold change) ≥ 1. b, c Shown are log2-transformed mean centred, normalized expression values. d Tracks represent merged reads of 3 replicates (4 replicates for Astr_2m). e Heatmaps show normalised ATAC read count of merged samples in 20 bp windows ±1  kb of peak centres. Shown are log2-transformed normalized expression values. See also Supplementary Data 9.