Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during wheat evolution

作者：Jingya Yuan, Haojie Sun, Yijin Wang, Lulu Li, Shiting Chen, Jiao Wu, Guanghong Jia, Longfei Wang, Junrong Mao, Zhongfu Ni, Xiue Wang, Qingxin Song · 发表于：Genome biology · 年份：2022 · DOI：10.1186/s13059-022-02611-3 · 被引用次数：45 · 研究领域：Chromosomal and Genetic Variations、Genomics and Chromatin Dynamics、Plant Molecular Biology Research

BACKGROUND: Bread wheat (Triticum aestivum) is an allohexaploid that is generated by two subsequent allopolyploidization events. The large genome size (16 Gb) and polyploid complexity impede our understanding of how regulatory elements and their interactions shape chromatin structure and gene expression in wheat. The open chromatin enrichment and network Hi-C (OCEAN-C) is a powerful antibody-independent method to detect chromatin interactions between open chromatin regions throughout the genome. RESULTS: Here we generate open chromatin interaction maps for hexaploid wheat and its tetraploid and diploid relatives using OCEAN-C. The anchors of chromatin loops show high chromatin accessibility and are concomitant with several active histone modifications, with 67% of them interacting with multiple loci. Binding motifs of various transcription factors are significantly enriched in the hubs of open chromatin interactions (HOCIs). The genes linked by HOCIs represent higher expression level and lower coefficient expression variance than the genes linked by other loops, which suggests HOCIs may coordinate co-expression of linked genes. Thousands of interchromosomal loops are identified, while limited interchromosomal loops (0.4%) are identified between homoeologous genes in hexaploid wheat. Moreover, we find structure variations contribute to chromatin interaction divergence of homoeologs and chromatin topology changes between different wheat species. The genes with discrepant chroma...