Fig. 5
LHX2 affects local and global chromatin accessibility by epistatic and steric regulation of transcription factors with high pioneer potential. a, b Correlation between LHX2 occupancy and local accessibility at LHX2 target sites in age-matched open chromatin regions in E14 and P2 control conditions and in Lhx2 cKO. Two-tailed t-test statistics is reported. For loss of accessibility statistics at LHX2 targets, refer to Supplementary Table 7. c, d Paired variations in gene expression and local chromatin accessibility are displayed for loci encoding LHX2 targeted transcription factors in embryonic Lhx2 cKO (Supplementary Data 3) (c) and developmentally regulated post natal targets (d). Representative transcription factors are highlighted with arrows (green/red for up/downregulation by RNA-Seq). e, f Correlation of open chromatin profiles obtained from ATAC-Seq flow-sorted fractions from control and Lhx2 cKO, normalized by the library size. Two-tailed t-test statistics is reported. For global loss of accessibility refer to Supplementary Table 8. g Cumulative distribution of differentially expressed transcription factors across intervals of pioneer potential. Transcription factors with predicted pioneer potential based on P2 RPCs accessibility profiles compared to E14 were identified and filtered based on RNA-Seq. Kolmogorov–Smirnov test was applied to putative pioneer TF with differential (blue) or comparable (red) expression between time points. Differentially expressed genes are distributed across higher intervals of pioneer potential than those shared between time points. h Footprint counts for individual transcription factors with predicted pioneer activity matching LHX2 co-occurrent motifs are shown in control and Lhx2 cKO from E14 and P2 retina. For predicted pioneer potential, refer to Supplementary Table 12
