Extended Data Fig. 2: Chromatin profiles of IEGs carrying the bipartite signature.

a, Fos, Egr1, Fosb and Nr4a3 genome browser views. ATAC (violet), H3K4me2 (yellow, E14.5 barrelette neurons), H3K4me3 (yellow, adult cortical neurons and cultured embryonic neurons), H3K27ac (red) and H3K27me3 (blue) are shown in E14.5 Drg11^{vPrV-ZsGreen/+} barrelette neurons, E15.5 embryonic cortical neural progenitors (NPC) and postmitotic neurons (PMID: 28793256), adult cortical excitatory neurons (PMID: 26087164), and embryonic cortical 7 day ex vivo cultured neurons (PMID: 20393465). Shaded boxes highlight promoters (pink) and gene bodies (blue). IEGs display a bipartite chromatin signature characterized by promoter-H3K27ac and gene body-H3K27me3 in E14.5 barrelette neurons and E15.5 cortical progenitors and postmitotic neurons. In contrast, H3K27me3 is not present on IEG gene bodies in postnatal cortical excitatory neurons, similar to postnatal barrelette neurons (see Fig. 3e and Extended Data Fig. 6b). Also, culturing embryonic cortical neurons for one week results in depletion of the H3K27me3 mark, similar to embryonic hindbrain neuron culture (see Extended Data Fig. 9a). In long genes (for example Nr4a3), H3K27me3 deposition on gene body does not stretch throughout the gene body, but is restricted only to the proximal region downstream of the promoter (also see Extended Data Fig. 3c). b, IEG (Fos, Egr1 and Fosb) genome browser views at E14.5, pre-fixed prior to the dissociation procedure. Shaded boxes highlight promoters (pink) and gene bodies (blue). The presence of the bipartite pattern (H3K27ac + promoter/H3K27me3+ gene body) in the pre-fixed tissue indicates that it is not induced by the dissociation procedure.