Regulatory elements in a Transcriptional Network Orchestrating Regional Patterning of Cortical Progenitors

To map enhancers involved in regional patterning of cortical progenitors, we performed TF ChIP for patterning transcription factors as well as assays for epigenomic marks and DNA accessibility in VZ cells purified from wild-type and patterning mutant mice. This integrated approach identified a cortical Regionalization TF network and VZ enhancers involved in cortical regional patterning. TF (EMX2, LHX2, NR2F1, PAX6, PBX1) and histone ChIP-Seq (H3K27ac and H3k27me3) and ATAC-Seq were conducted on mouse cortex at E12.5.TF ChIP-seq was conducted on microdissected cortex. Histone ChIP-Seq and ATAC-Seq was conducted on VZ purified cells (using FlashTag methods) in WT and patterning mutant mice (Emx2 KO, Pax6 KO, Nr2f1 KO).