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The rice AT-rich pincer-like element family of conserved noncoding sequences regulates chromatin loop formation

文献类型： 外文期刊

作者： Xu, Yonghan 1 ; Wu, Dechuan 1 ; Zhao, Manman 1 ; Tang, Wei 3 ; Cheng, Xiang 1 ; Hu, Qunwen 1 ; Liu, Zhiwei 1 ; Gan, Jiangtao 1 ; Hua, Jiahao 1 ; Zou, Guoxing 4 ; Lu, Ai 1 ; Yang, Chen 1 ; Zheng, Yunxing 1 ; Li, Wenjin 1 ; Li, Jincai 1 ; Wang, Xiaobo 1 ; Ma, Chuanxi 1 ;

作者机构： 1.Anhui Agr Univ, Sch Agron, Hefei 230036, Peoples R China

2.Anhui Agr Univ, Jinzhai Modern Agr Cooperat Ctr, Integrated Expt Stn Dabie Mt, Luan 237000, Peoples R China

3.Anhui Agr Univ, Coll Hort, Hefei 230036, Peoples R China

4.Jiangxi Acad Agr Sci, Rice Res Inst, Nanchang 330200, Peoples R China

期刊名称：PLANT PHYSIOLOGY （ 影响因子：6.9； 五年影响因子：7.7 ）

ISSN： 0032-0889

年卷期： 2025 年 198 卷 2 期

页码：

收录情况： SCI

摘要： The comprehensive annotation of regulatory elements in linear genomes is needed to elucidate the molecular mechanisms underlying chromatin loop formation in plants. Here, we characterized a novel family of conserved noncoding sequences (CNSs) in the rice (Oryza sativa) genome. These sequences, known as AT-rich pincer-like elements (APEs), are composed of 13-bp repeat unit arrays in a reverse-forward configuration. Our findings revealed that there are 611 APE copies across the japonica genome. Deletion of single APEs disrupted the long-range chromatin loops anchoring target-APE regions and moderately remodeled the profile of A/B compartments, topologically associating domains (TADs), and chromatin loops, thereby rewiring the expression of looped gene(s) including those controlling important agronomic traits. Thus, APEs function as hub motifs directly mediating chromatin looping and maintaining 3D genome integrity and stability at the levels of compartments, TADs, and loops. Moreover, neighboring genomic regions harboring numerous paired non-APE (NA) CNSs were more likely to interact with each other. This finding suggests that NA CNS pairs might play a helper role in determining loop frequency in a dose-dependent manner, likely by ensuring the pairing selectivity of anchor sites. Our study highlights the importance of APEs and NA CNSs in maintaining 3D genome structure, thereby providing the framework required to link many noncoding repetitive elements to their molecular functions in plants. AT-rich pincer-like elements (APEs) and non-APE conserved noncoding sequences maintain 3D genome structure by regulating chromatin loop formation.

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