数字农科院2.0

Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits

文献类型： 外文期刊

作者： Tao Zhu;Chunjiao Xia;Ranran Yu;Xinkai Zhou;Xingbing Xu;Lin Wang;Zhanxiang Zong;Junjiao Yang;Yinmeng Liu;Luchang Ming;Yuxin You;Dijun Chen;Weibo Xie

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关键词： （0-1-5）

期刊名称： Nature Communications

ISSN： 2041-1723

年卷期： 2024 年 15 卷 1 期

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收录情况： SCIE（2024版）

摘要： Unraveling the regulatory mechanisms that govern complex traits is pivotal for advancing crop improvement. Here we present a comprehensive regulome atlas for rice (Oryza sativa), charting the chromatin accessibility across 23 distinct tissues from three representative varieties. Our study uncovers 117,176 unique open chromatin regions (OCRs), accounting for ~15% of the rice genome, a notably higher proportion compared to previous reports in plants. Integrating RNA-seq data from matched tissues, we confidently predict 59,075 OCR-to-gene links, with enhancers constituting 69.54% of these associations, including many known enhancer-to-gene links. Leveraging this resource, we re-evaluate genome-wide association study results and discover a previously unknown function of OsbZIP06 in seed germination, which we subsequently confirm through experimental validation. We optimize deep learning models to decode regulatory grammar, achieving robust modeling of tissue-specific chromatin accessibility. This approach allows to predict cross-variety regulatory dynamics from genomic sequences, shedding light on the genetic underpinnings of cis-regulatory divergence and morphological disparities between varieties. Overall, our study establishes a foundational resource for rice functional genomics and precision molecular breeding, providing valuable insights into regulatory mechanisms governing complex traits.

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