biostudies-literatureLi YDevelopment funds of the National Key Laboratory of Crop Genetic ImprovementHubei Provincial Postdoctoral Innovative Talent Cultivation ProgramFundamental Research Funds for the Central UniversitiesHubei Provincial Natural Science Foundation for Young Scholars ProjectHubei Hongshan Laboratory Start FundNational Natural Science Foundation of ChinaChina Postdoctoral Science FoundationNational Key Research and Development Program of Hubei ProvinceBiological Breeding-National Science and Technology Major ProjectPostdoctoral Fellowship Program of CPSFDepartment of Human Resources and Social Security of Hubei Province58https://www.ebi.ac.uk/biostudies/studies/S-EPMC12930761biostudies-literatureUnknown27(1)<h4>Background</h4>Trimethylation of histone H3 lysine 27 (H3K27me3) confers a repressive chromatin state and is dynamically deposited and removed to regulate gene expression throughout plant growth and development. Nevertheless, the three-dimensional epigenome architecture linked to H3K27me3 and its regulatory role in controlling rice development remain unclear.<h4>Results</h4>Here, we employ long-read ChIA-PET to map the genome topology associated with H3K27me3 in rice, identifying hundreds of repressive chromatin spatial clusters within chromosomes. The T-DNA insertional mutagenesis of EMBRYONIC FLOWER 2b (OsEMF2b) leads to disruption of H3K27me3-associated chromatin interaction networks. Notably, we discover that the three key flowering time loci, Early heading date 1 (Ehd1) and HeadinGenome biology3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice.PMC129307612662024SKPY002, 2662023SKQD0022025AFB3772023ZD040762022BBA542023HSQD0025903201032022T150245, 2022M71126432470669, 32200424WHGZ23212024HBBHCXB031GZC20240563, GZC20240554Li GLi HYan JOuyang WOuyang XXing YChen GWu CZheng RXie LShen CGuan PFoda MQiu LWu HLi WGuo MLi XLi YZhang ZCao ZWang SZhang YHuang Xfalse3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice.<h4>Background</h4>Trimethylation of histone H3 lysine 27 (H3K27me3) confers a repressive chromatin state and is dynamically deposited and removed to regulate gene expression throughout plant growth and development. Nevertheless, the three-dimensional epigenome architecture linked to H3K27me3 and its regulatory role in controlling rice development remain unclear.<h4>Results</h4>Here, we employ long-read ChIA-PET to map the genome topology associated with H3K27me3 in rice, identifying hundreds of repressive chromatin spatial clusters within chromosomes. The T-DNA insertional mutagenesis of EMBRYONIC FLOWER 2b (OsEMF2b) leads to disruption of H3K27me3-associated chromatin interaction networks. Notably, we discover that the three key flowering time loci, Early heading date 1 (Ehd1) and Headin2026-01-01T00:00:00Z2026 Jan2026-07-09T12:21:39.814Z2026-07-09T11:17:34.682ZS-EPMC129307614160664310.1186/s13059-026-03940-3