Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations
2021
Zhang, Xingguo | Pandey, Manish K. | Wang, Jianping | Zhao, Kunkun | Ma, Xingli | Li, Zhongfeng | Zhao, Kai | Gong, Fangping | Guo, Baozhu | Varshney, Rajeev K. | Yin, Dongmei
BACKGROUND: Three-dimensional (3D) chromatin organization provides a critical foundation to investigate gene expression regulation and cellular homeostasis. RESULTS: Here, we present the first 3D genome architecture maps in wild type and mutant allotetraploid peanut lines, which illustrate A/B compartments, topologically associated domains (TADs), and widespread chromatin interactions. Most peanut chromosomal arms (52.3%) have active regions (A compartments) with relatively high gene density and high transcriptional levels. About 2.0% of chromosomal regions switch from inactive to active (B-to-A) in the mutant line, harboring 58 differentially expressed genes enriched in flavonoid biosynthesis and circadian rhythm functions. The mutant peanut line shows a higher number of genome-wide cis-interactions than its wild-type. The present study reveals a new TAD in the mutant line that generates different chromatin loops and harbors a specific upstream AP2EREBP-binding motif which might upregulate the expression of the GA2ox gene and decrease active gibberellin (GA) content, presumably making the mutant plant dwarf. CONCLUSIONS: Our findings will shed new light on the relationship between 3D chromatin architecture and transcriptional regulation in plants.
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