Fig. 2
DNA sequence and methylation variation correlate with differential BZR1 binding. a Schematics of HASCh-seq approach and possible causes for allele-specific binding events. Chromatin-IP is performed in F1 hybrid plants. Possible scenarios for TF binding to the parental genomes (green and blue) are depicted. Binding strength is depicted by the black arrows width: (top) with no alteration in motif or chromatin structure, binding is expected to be equal. Lower binding is expected if the motif is altered (middle) or epigenetics like DNA methylation (bottom) vary between alleles. b Example of allele-specific ZmBZR1 binding near Zm00001eb034870. ZmBZR1 bound reads that map uniquely to B73 (green) or Mo17 (blue) are shown. c Distribution of SNPs with a significant allelic bias to either B73 or Mo17 located within BZR1 peaks. d Allelic and spatial distribution of ASBs with a bias towards B73 (green) or Mo17 (blue) along the B73 chromosomes. Allelic bias is expressed as a percentage of B73 read counts. Chromosome borders and length are depicted by dashed lines and arrows, respectively. Centromeres are indicated by orange rectangles. A red box highlights the ASB near Zm00001eb034870 displayed in b. e Genomic distribution of ASBs classified according to their location relative to genes. In case of two genes in the proximity of an ASB, the priority given was exon>intron>UTR>1 kb upstream>1 kb downstream>1–5 kb upstream. e Frequency of BRREs (CGTG[C/T]G), G-box (CACGTG), and a control motif CCGTAC (SBP-box) around ASBs of the alleles with higher BZR1 binding. g Fraction of ASBs overlapping with motifs, for which the allele with canonical BRRE, G-box or control motifs GCCGCC (GCC-box), and SBP-box showed higher ZmBZR1 affinity. Both BZR1-related motifs, but not the control motifs, diverge significantly (p<0.001, Fisher’s exact test) from the expected 50% random distribution. h Correlation of haplotype-specific DNA methylation differences at ASB loci between B73/Mo17 parental alleles and B73/Mo17 F1 alleles (r Pearson correlation). i ASBs affecting ZmBZR1 binding motifs and/or overlapping with allele-specific methylation differences (CpG, CHG, or CHH) in the F1. k–m Average k CpG, l CHG, and m CHH methylation frequency in B73 (green) and Mo17 (blue) over ASB loci with a least 85% binding bias towards B73 or Mo17. High-affinity (___) and low-affinity (….) alleles are separated by genotype. n–p Correlation of CG (n), CHG (o), and CHH (p) methylation with allele-specific ZmBZR1 binding. Average B73-Mo17 methylation of the 20-bp surrounding ASBs are plotted against the allelic bias (expressed in percentage of B73 read counts). Significant methylation differences are indicated by red dots