Journal article
Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations
Genome Biology, Vol.22(1), Art. 315
2021
Abstract
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.
Details
- Title
- Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations
- Authors/Creators
- X. Zhang (Author/Creator) - Henan Agricultural UniversityM.K. Pandey (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsJ. Wang (Author/Creator) - University of FloridaK. Zhao (Author/Creator) - Henan Agricultural UniversityX. Ma (Author/Creator) - Henan Agricultural UniversityZ. Li (Author/Creator) - Henan Agricultural UniversityK. Zhao (Author/Creator) - Henan Agricultural UniversityF. Gong (Author/Creator) - Henan Agricultural UniversityB. Guo (Author/Creator) - Agricultural Research ServiceR.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsD. Yin (Author/Creator) - Henan Agricultural University
- Publication Details
- Genome Biology, Vol.22(1), Art. 315
- Publisher
- BioMed Central
- Identifiers
- 991005542775207891
- Copyright
- © 2021 The Authors.
- Murdoch Affiliation
- Centre for Crop and Food Innovation; Food Futures Institute; State Agricultural Biotechnology Centre
- Language
- English
- Resource Type
- Journal article
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- Citation topics
- 1 Clinical & Life Sciences
- 1.54 Molecular & Cell Biology - Genetics
- 1.54.100 Epigenetic Regulation
- Web Of Science research areas
- Biotechnology & Applied Microbiology
- Genetics & Heredity
- ESI research areas
- Molecular Biology & Genetics