Extended Data Figure 4 : Examples of REST+ cCRE categories

Extended Data Figure 4 | Examples of REST+ cCRE categories

a, Genome browser view of REST+ enhancer/silencer EH38E2130108. EH38E2130108 has high REST ChIP-seq signal (purple), moderate DNase signal (green), and low H3K27ac signal (yellow) in K562, which results in it being classified as CA-TF in K562. For in vitro-differentiated neurons, EH38E2130108 is classified as an enhancer because it has high DNase and H3K27ac signals. The black bar denotes the genomic region tested in the transgenic mouse enhancer assay. b, Density plot of STARR scores calculated by CAPRA for all cCREs (black) and REST+ distal enhancer cCREs (yellow). Dashed line indicates the STARR score for EH38E2130108. c, Representative transgenic mouse enhancer assay results for EH38E2130108 (activity in 3/4 tested embryos). Dashed circle indicates activity in hindbrain (2/4), midbrain (2/4), and forebrain (2/4). d, Genome browser view of REST+ CA-TF EH38E4127779 with biochemical signals as defined in panel a. EH38E4127779 has high REST ChIP-seq signal, moderate DNase signal, and low H3K27ac signal in K562, which results in it being classified as CA-TF in K562. In in vitro-differentiated neurons, EH38E4127779 has no enhancer signatures and showed no activity in the transgenic mouse enhancer assay. e, Density plot of the distributions of STARR scores calculated by CAPRA for all cCREs (black) and REST+ CA-TF cCREs (purple). Dashed line indicates STARR score for EH38E4127779. f, No positive results we observed from testing EH38E4127779 in the transgenic mouse enhancer assay.