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However, bonafide genome organizers have not been identified in plants. Here, we show that EMBRYONIC FLOWER1 (EMF1) functions as a genome modulator in Arabidopsis. EMF1 interacts with the cohesin component SISTER CHROMATIN COHESION3 (SCC3) and both proteins are enriched at compartment domain (CD) boundaries. Accordingly, emf1 and scc3 show a strength decrease in CD boundary in which these proteins colocalize. EMF1 maintains CD boundary strength either independently or in cooperation with histone modifications. Moreover, EMF1 is required to maintain gene-resolution interactions and to block long-range aberrant chromatin loops. These data unveil a key role of EMF1 in regulating 3D chromatin structure.ENAnuclear chromatin, cytoplasmic chromatin, Arabidopsis, Arabidopsis thalianas, Cresses, A., A. thalianas, chromosome scaffold, thalianas, Arabidopsis thaliana, Mouse-ear Cress, Cress, thaliana, Mouse ear, A. thaliana, Arabidopses, Mouse-ear Cresses, Chromatins, Mouse-ear, Cardaminopsis.nuclear chromatin, cytoplasmic chromatin, Arabidopsis, Arabidopsis thalianas, Cresses, A., A. thalianas, chromosome scaffold, thalianas, Arabidopsis thaliana, Mouse-ear Cress, Cress, thaliana, Mouse ear, A. thaliana, Arabidopses, Mouse-ear Cresses, Chromatins, Mouse-ear, Cardaminopsis.falseEMF1 functions as a 3D chromatin modulator in ArabidopsisEMF1 functions as a 3D chromatin modulator in Arabidopsis2024-11-192024-11-19PRJEB60957