Fig. 1: Secondary structure mapping of selected mouse neuronal enhancer RNAs.

The mouse Nr4a1 (a) and Arc (b) gene and enhancer loci in genome browser view. Exo-, GRO-, and mRNA-seq signal from KCl-stimulated mouse cortical neurons is plotted alongside Pol II (8WG16 antibody), CBP, and H3K27ac ChIP-Seq data from publicly available sources^{3, 20}. A zoom-in view of the Exo-seq data attests to the single-nucleotide resolution in determining eRNA TSSs (eTSS). The enhancer locus of Nr4a1 revealed two distinct TSS sites (eTSS-(a) and eTSS-(b)). c SHAPE reactivity profile of Arc eRNA (1–200), as computed by using Shapemapper2²⁸. Using the experimentally determined SHAPE reactivities as restraints, the corresponding secondary structure (shown below) was generated with RNAStructure²⁹. Nucleotides are shown as circles and are colored according to their SHAPE reactivity (see the reactivity scale bar above the structure). d The distribution of median SHAPE reactivities for all individual 39 eRNAs that were subjected to SHAPE-MaP is summarized in a boxplot, showing individual data points (n = 39). Data points corresponding to prominent immediate early genes are marked in red. eRNAs that exhibit low median SHAPE reactivities (<0.1) are considered to be highly structured. e, f Secondary structures of variant (b) and variant (a) of Nr4a1 eRNAs (1–200). Determined and plotted as in (c). Source data for (c, d) are provided in a Source Data file.