Extended Data Fig. 7: Peak positional variation among genotypes.
From: Transcription factor binding divergence drives transcriptional and phenotypic variation in maize
a, Comparative JBrowse2 genome browser view showing shared peaks of B73 and Mo17 at the MADS67 locus. b, JBrowse2 genome browser view showing TF binding site positional variants at the ZmATL34 locus. Lower heatmap shows ZmATL34 RNA expression levels (transcripts per million) from several tissues40. A 13-fold increase in Mo17 RNA expression was observed in radicle tissue compared to B73. c, Top: percentage of shared TF diversity panel promoter peaks (top 20%) that correspond to positional variants (PosV) greater than 500 bp or less than 500 bp. Bottom: percentage of top (shared and specific) promoter peaks that corresponded to shared PosVs or B73-specific peaks. Each datapoint corresponds to an individual TF, n = 65. Whiskers indicate the minimum and maximum values; central lines correspond to medians and box boundaries denote the upper (25th percentile) and lower (75th percentile) quartiles. d, Plot showing percentage of B73-Mo17 shared promoter peaks (<-10kb) that were associated with differentially expressed genes in various tissues from40. Genes associated with PosV<500 bp peaks are shown in dark pink, while those associated with PosV>500 peaks are shown in light pink. Fisher’s exact tests were performed to assess the enrichment of DEGs in PosV>500 bp genes relative to PosV<500 bp genes for each TF and tissue combination, and the resulting p-values were adjusted for multiple testing. e, Heatmap of -log10 FDR-adjusted p-values from one-sided Fisher’s exact tests, evaluating whether root cell type marker genes determined by single cell RNA-seq data41 are enriched for putative target genes associated with DAP-seq peaks shared between B73 and Mo17, compared to putative targets of B73-specific peaks.
