Fig. 7

Yy1 controls a similar gene set throughout cortex development. a Genome-wide binding of Yy1 to DNA regions was analyzed by chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) of cortex cells derived at E15.5. Statistical analysis of the enriched regions identified 246 binding events at E15.5 (FDR < 0.001), present in at least 1 of 2 replicas. b Homer motif discovery revealed the known Yy1-binding motif as the highest scoring motif (p < 1*e-50). c–e Read cluster profile and distribution of binding sites to different genomic locations at E15.5. Yy1 binds preferentially to the promoter region of the transcription start site (TSS) of genes. f Analysis of overlap between E12.5 and E15.5 ChIP-seq data. g RNA-seq comparing E15.5 Yy1iKO vs control (each n = 3 embryos) radial glia cells from the dorsal cortex which were isolated by microdissection and subsequent Prominin1-based (CD133-FITC) FACS. A total of 1080 genes were downregulated (660 genes) or upregulated (420 genes) upon induced knockout of Yy1 (|log2 fold change| > 0.32, p < 0.05, FDR < 0.05). h RNA-seq expression of genes at E11.5 and E15.5, which are bound by at E12.5 and E15.5, upon knockout of Yy1. *p < 0.05