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 [CUT&Tag]

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. Overall design: Toinvestigate PLT function involved in gene expression and chromatin modification in rice root meristem,we performed CUT&Tag sequencing and RNA-seq using root tip (approx. 0.8 cm) of 7-day wild type and plt345 plants.