Fig. 5

Yy1 directly binds to metabolic genes. a Genome-wide binding of Yy1 to DNA regions was analyzed by chromatin immunoprecipitation against Yy1 followed by sequencing (ChIP-seq) of cortex cells derived at E12.5. Statistical analysis of the enriched regions identified 464 binding events at E12.5 (FDR < 0.001), present in at least 1 of 2 replicas. b Homer motif discovery revealed a known Yy1-binding motif as the highest scoring motif (p < 1*e-50). c Read cluster profile reveals preferential binding of Yy1 close to the transcription start site (TSS) of target genes. d Distribution of binding sites to different genomic locations. Yy1 binds preferentially to the promoter region of the transcription start site (TSS) of genes. e Gene Ontology (GO) term network analysis on the basis of Yy1-bound target genes at E12.5. Each node represents an enriched GO term (adjusted p value (Corrected with Bonferroni step down procedure) < 0.05). Nodes are interconnected when the gene overlap is > 50%, based on the kappa score. BP, biological process; MF, molecular function; CC, cellular component. A fully labeled version of the network is given in Supplementary Fig. 8. f, g Genomic snapshots depicting Yy1-binding events at metabolic genes (g) and genes involved in protein translation (f). kb, kilo bases