Conserved H3K27me3-associated chromatin looping mediates physical interactions of gene clusters in plants
Conserved H3K27me3-associated chromatin looping mediates physical interactions of gene clusters in plants
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DOI：
10.1111/jipb.13502
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发表时间：
2023-06-07
影响因子：
11.4
通讯作者：
Qian，Weiqiang
中科院分区：
文献类型：
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作者：
Sun，Linhua;Cao，Yuxin;Qian，Weiqiang
高阶染色质组织对于转录调控、基因组稳定性维持和其他基因组功能至关重要。越来越多的证据表明，植物和动物之间的3D染色质组织存在显着差异。然而，植物中染色质组织的程度、模式和规则仍然不清楚。在这项研究中，我们系统地确定和表征了长距离染色质环在thetiopsis 3D基因组。我们鉴定了数百个长距离异染色质环，并发现它们的锚区与H3K27me3表观遗传修饰密切相关。此外，我们证明了这些染色质环依赖于Polycomb组（PcG）蛋白，这表明Polycomb抑制复合物2（PRC2）复合物对于建立和维持这些新的环是必不可少的。虽然大多数这些PcG介导的染色质环是稳定的，但其中许多环是组织特异性的或受不同治疗的动态调节。有趣的是，串联排列的基因簇和代谢基因簇在锚区富集。H3K27me3标记的长距离染色质相互作用与特定基因簇的共调控相关。最后，我们还在水稻和大豆中鉴定了与基因簇相关的H3K27me3相关染色质环，表明这些长距离染色质环在植物中是保守的。我们的研究结果为植物基因组进化和转录协同调节提供了新的见解。
Higher‐order chromatin organization is essential for transcriptional regulation, genome stability maintenance, and other genome functions. Increasing evidence has revealed significant differences in 3D chromatin organization between plants and animals. However, the extent, pattern, and rules of chromatin organization in plants are still unclear. In this study, we systematically identified and characterized long‐range chromatin loops in theArabidopsis3D genome. We identified hundreds of long‐rangecischromatin loops and found their anchor regions are closely associated with H3K27me3 epigenetic modifications. Furthermore, we demonstrated that these chromatin loops are dependent on Polycomb group (PcG) proteins, suggesting that the Polycomb repressive complex 2 (PRC2) complex is essential for establishing and maintaining these novel loops. Although most of these PcG‐medicated chromatin loops are stable, many of these loops are tissue‐specific or dynamically regulated by different treatments. Interestingly, tandemly arrayed gene clusters and metabolic gene clusters are enriched in anchor regions. Long‐range H3K27me3‐marked chromatin interactions are associated with the coregulation of specific gene clusters. Finally, we also identified H3K27me3‐associated chromatin loops associated with gene clusters inOryza sativaandGlycine max, indicating that these long‐range chromatin loops are conserved in plants. Our results provide novel insights into genome evolution and transcriptional coregulation in plants.