期刊
HORTICULTURE RESEARCH
卷 8, 期 1, 页码 -出版社
OXFORD UNIV PRESS INC
DOI: 10.1038/s41438-021-00494-2
关键词
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资金
- National Natural Science Foundation of China [31922061, 41871044, 31500502, 31561123001, 31590821]
- US National Science Foundation [DEB-1542599]
- National Key Research and Development Program of China [2016YFD0600101, 2017YFC0505203]
- National Science and Technology Major Project [2018ZX10201002]
- National Key Project for Basic Research [2012CB114504]
- Fundamental Research Funds for the Central Universities [2020SCUNL103, 2018CDDY-S02-SCU, SCU2019D013]
This study investigates the chromatin organization and gene regulation in two poplar species after whole-genome duplication (WGD), revealing low conservation of hierarchical chromatin organization across the species. The divergence of gene expression between WGD-derived paralogs is associated with chromatin interactions, and colocalized paralogs show strong similarities in epigenetic modifications and expression levels, suggesting a correlation between spatial localization of duplicated genes and biased expression during diploidization. This study provides insights into the evolution of chromatin organization and transcriptional regulation in poplars during speciation after WGD.
The nonrandom three-dimensional organization of chromatin plays an important role in the regulation of gene expression. However, it remains unclear whether this organization is conserved and whether it is involved in regulating gene expression during speciation after whole-genome duplication (WGD) in plants. In this study, high-resolution interaction maps were generated using high-throughput chromatin conformation capture (Hi-C) techniques for two poplar species, Populus euphratica and Populus alba var. pyramidalis, which diverged similar to 14Mya after a common WGD. We examined the similarities and differences in the hierarchical chromatin organization between the two species, including A/B compartment regions and topologically associating domains (TADs), as well as in their DNA methylation and gene expression patterns. We found that chromatin status was strongly associated with epigenetic modifications and gene transcriptional activity, yet the conservation of hierarchical chromatin organization across the two species was low. The divergence of gene expression between WGD-derived paralogs was associated with the strength of chromatin interactions, and colocalized paralogs exhibited strong similarities in epigenetic modifications and expression levels. Thus, the spatial localization of duplicated genes is highly correlated with biased expression during the diploidization process. This study provides new insights into the evolution of chromatin organization and transcriptional regulation during the speciation process of poplars after WGD.
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