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Transcription factors PLT and chromatin regulators PRC2 and JMJ703 form nuclear condensates to maintain gene repression in bivalent domains controlling cell fate in rice root meristem [RNA-Seq]

ABSTRACT: The maintenance of stem cells within root meristem is the foundation for continuous growth of the root system. The PLETHORA (PLT) transcription factors have a function to control patterning of root stem cell niche, but the mechanism by which PLTs regulate root meristem activity remains unclear. In this work we show that rice PLT3, PLT4 and PLT5 function redundantly to maintain the stem cell pool of root meristem by repressing the expression of cell growth/development-promoting genes, which display a bivalent histone methylation feature marked by both H3K27me3 and H3K4me3 in root meristem cells. Mass spectrometry and protein interaction assays revealed that PLT5 could interact with core components of Polycomb Repressive Complex 2 (PRC2) that deposits H3K27me3 and the H3K4me3 demethylase JMJ703 in rice cells. In addition, JMJ703 could also interact with the PRC2 catalytic subunit SDG718. Loss of function of PLT3, PLT4 and PLT5 resulted in decreased H3K27me3, increased H3K4me3, and reduced PRC2 binding in bivalent genes in root meristem. Importantly we show that PLT5, PRC2 and JMJ703 could form a tripartite complex within nuclear condensates likely through PTL5 and/or JMJ703-induced phase-separation. These results uncover a chromatin mechanism by which PLTs control the patterning of stem cell niche in rice root meristem.

ORGANISM(S): Oryza sativa Japonica Group

PROVIDER: GSE251803 | GEO | 2025/11/18

REPOSITORIES: GEO

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Project description:The ability of cells to perceive and translate versatile cues into differential chromatin and transcriptional states is critical for many biological processes1-4. In plants, timely transition to a flowering state is crucial for successful reproduction5-7. EARLY BOLTING IN SHORT DAY (EBS) is a negative transcriptional regulator that prevents premature flowering in Arabidopsis8,9. Here, we revealed that bivalent bromo-adjacent homology (BAH)-plant homeodomain (PHD) reader modules of EBS bind H3K27me3 and H3K4me3, respectively. A subset of EBS-associated genes was co-enriched with H3K4me3, H3K27me3, and the Polycomb repressor complex 2 (PRC2). Interestingly, EBS adopts an auto-inhibition mode to mediate its binding preference switch between H3K27me3 and H3K4me3. This binding balance is critical because disruption of either EBS-H3K27me3 or EBS-H3K4me3 interaction induces EBS-mediated early floral transition. This study identifies a single bivalent chromatin reader capable of recognizing two antagonistic histone marks and reveals a distinct mechanism of interplay between active and repressive chromatin states.The ability of cells to perceive and translate versatile cues into differential chromatin and transcriptional states is critical for many biological processes1-4. In plants, timely transition to a flowering state is crucial for successful reproduction5-7. EARLY BOLTING IN SHORT DAY (EBS) is a negative transcriptional regulator that prevents premature flowering in Arabidopsis8,9. Here, we revealed that bivalent bromo-adjacent homology (BAH)-plant homeodomain (PHD) reader modules of EBS bind H3K27me3 and H3K4me3, respectively. A subset of EBS-associated genes was co-enriched with H3K4me3, H3K27me3, and the Polycomb repressor complex 2 (PRC2). Interestingly, EBS adopts an auto-inhibition mode to mediate its binding preference switch between H3K27me3 and H3K4me3. This binding balance is critical because disruption of either EBS-H3K27me3 or EBS-H3K4me3 interaction induces EBS-mediated early floral transition. This study identifies a single bivalent chromatin reader capable of recognizing two antagonistic histone marks and reveals a distinct mechanism of interplay between active and repressive chromatin states.v

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Transcription factors PLT and chromatin regulators PRC2 and JMJ703 form nuclear condensates to maintain gene repression in bivalent domains controlling cell fate in rice root meristem [RNA-Seq]

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