Hybrid allele-specific ChIP-Seq (HaschSeq) analysis links variation in transcription factor binding to traits in maize
Variation in transcriptional regulation is a major cause of phenotypic diversity1 . Genomewide association studies (GWAS) have shown that most functional variants reside in noncoding regions, where they potentially affect transcription factor (TF) binding and chromatin accessibility to alter gene expression. Pinpointing such regulatory variations, however, remains challenging2. Here, we developed a hybrid allele-specific chromatin binding sequencing (HASCh-seq) approach and identified variations in target binding of the brassinosteroid (BR) responsive transcription factor ZmBZR1 in maize. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) in B73xMo17 F1s identified thousands of target genes of ZmBZR1. Allele-specific ZmBZR1 binding (ASB) was observed for about 14.3% of target genes. It correlated with over 550 loci containing sequence variation in BZR1-binding motifs and over 340 loci with haplotype-specific DNA methylation, linking genetic and epigenetic variations to ZmBZR1 occupancy. Comparison with GWAS data linked hundreds of ASB loci to important yield, growth and disease-related traits. Our study provides a robust method for analyzing genome-wide variations of transcription factor occupancy and identified genetic and epigenetic variations of the BR response transcription network in maize.
Link to datasets, tmp and output files: https://1drv.ms/u/s!Avm82Xhe9EZj62fdhHXuxu3W-F2J?e=JUQImJ