Epigenomics of Neural Cells: REST-Induced Down- and Upregulation of Gene Expression in a Two-Clone PC12 Cell Model

Figure 2

Enrichment analyses of hrPC12 signatures based on available ChIP-Seq datasets and ENCODE TF data derived from cell lines of various types. (a) Among the genes identified by RNA-Seq as down- and upregulated, the ChIP-Seq enrichment analyses distinguished two families, one composed of the genes possibly regulated directly by REST (REST targets) and the other regulated indirectly or by other mechanisms (non-REST targets). (b) The down- and upregulated genes analyzed together were separated as possible REST targets (YES) and nontargets (NO), illustrated as box-whiskers in terms of median fold distribution of the hrPC12/wtPC12 log₂ ratios. Notice that the notches, corresponding to the median log₂ ratios, are negative (−2.7) for the targets and positive (1.9) for the nontargets. (c) illustrates the phenotypic pathways of possible downregulated REST target genes exhibiting significant ChIP-Seq enrichment. The green circle numbers correspond to the following pathways: 1–12: synaptic transmission; 13: excitability: 14–17: cell-cell signaling; 18–20: axonal guidance; 21: SIDS syndrome, including neural-specific TFs and receptors.

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