Experiments were performed using the striatum of male and female Q140 and WT mice at 6 months of age, and targeting super enhancer-regulated genes downregulated in HD striatum, including Pde10a, Gpr6 and Ptpn5, and non-super enhancer-regulated genes such as Msh2, as a control (Fig. 4a, b, Supplementary Figs. 15, 16a–c and Supplementary Data 2). Here, PTPN5 is linked to Huntington disease.