Fig. 1: Analysis of chromatin interactions in F1 hybrids and their parental lines.
From: Conservation and variability of long-range interactions in structurally diverse maize genomes
a Overview of the datasets we generated and contents to be explored in this study. By using newly generated HiChIP, ChIP-seq, and corresponding RNA-seq data, we would detect inbred-specific, hybrid-specific, and inter-allelic interactions; and then aimed to investigate how structure variations (SVs) contribute to inbred-specific interactions, how hybrid-specific ones regulate gene expression, and are there any inter-allelic ones existed in the maize hybrids. Some interactive examples were further confirmed by 4C-seq. b, c Comparisons of the number of uniquely mapped reads (b) and the number of peaks (c) obtained, when aligning B73 or Mo17 inbred ChIP-seq data to their cognate and counterpart reference genomes, respectively. d, e Comparisons of the number of valid read pairs (d) and the number of interactions (e) we obtained when aligning HiChIP datasets of individual inbred lines to their cognate and counterpart reference genomes. B73 data was mapped to B73 and B73-SNP substituted Mo17 reference genome, and Mo17 data was mapped to Mo17 and Mo17-SNP substituted B73 reference genome. B73-ref, B73 reference genome (B73_AGPv4); Mo17-ref, Mo17 reference genome (Mo17-CAU-v1). For b-e, B73-R1 indicates the replicate 1 dataset of B73 while B73-R2 for the replicate 2 of B73 for H3K4me3 or H3K27ac; Mo17-R1 and Mo17-R2 have the same meanings. f Pipeline of long-range interaction detection using combined B73 + Mo17 reference genome. Taking B73 inbred as an example of inbred samples, the HiChIP data will be aligned to the B73_AGPv4 genome and Mo17-CAU-v1 with B73-SNP substituted, respectively. All the valid read pairs along 20 chromosomes, as well as their corresponding peaks obtained based on ChIP-seq data, will be utilized to call loops using FitHiChIP; by contrast, the pipeline for hybrids was quite similar, except that the HiChIP data being aligned to B73_AGPv4 genome and Mo17-CAU-v1, respectively. B73-ref and Mo17-ref have the same meaning as in (b).
