J-domain proteins stimulate PKL-mediated chromatin compaction at H3K4-hypomethylated genomic loci

Guan, B.-B.; Yan, Z.; Du, P.; Sia, Y.; Yuan, D.-Y.; Luo, Y.-X.; Li, J.-X.; Su, X.-M.; Su, Y.-N.; Guo, J.; Liu, Z.-Z.; Liu, X.-Y.; Li, L.; Chen, S.; Chen, Z.; He, X.-J.

doi:10.64898/2026.09.14.751395

bioRxiv · 10.64898/2026.09.14.751395

J-domain proteins stimulate PKL-mediated chromatin compaction at H3K4-hypomethylated genomic loci

Guan, B.-B.·Yan, Z.·Du, P.·Sia, Y.·Yuan, D.-Y.·Luo, Y.-X.·Li, J.-X.·Su, X.-M.·Su, Y.-N.·Guo, J.·Liu, Z.-Z.·Liu, X.-Y.·Li, L.·Chen, S.·Chen, Z.·He, X.-J.

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Abstract

Chromatin accessibility varies widely across distinct genomic regions in eukaryotes, yet the mechanisms governing these differential patterns remain poorly understood. Here, we identify a subfamily of functionally redundant J-domain proteins (JDPs) that assemble into a protein complex with PICKLE (PKL), an evolutionarily conserved CHD3-type chromatin remodeler, in Arabidopsis thaliana. JDPs are required not only for maintaining PKL protein stability but also for stimulating its nucleosome remodeling and ATPase activities. A previously uncharacterized histone-binding domain (HBD) within JDPs specifically recognizes the N-terminal tail of histone H3 when the H3K4me3 modification is absent. This interaction enhances PKL-mediated nucleosome sliding and ATPase activities in vitro, and promotes PKL-dependent chromatin compaction at H3K4me3-depleted genomic loci in vivo. The PKL-JDP complex drives chromatin compaction to repress developmentally regulated genes, thereby governing key developmental phase transitions, including the embryo-to-seedling transition and flowering. Collectively, these findings uncover a distinct mechanism by which the absence of H3K4me3 is sensed to initiate regional chromatin compaction, repress developmentally regulated genes, and facilitate key developmental transitions.

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Guan, B.-B., Yan, Z., Du, P., Sia, Y., Yuan, D.-Y., Luo, Y.-X., Li, J.-X., Su, X.-M., Su, Y.-N., Guo, J., Liu, Z.-Z., Liu, X.-Y., Li, L., Chen, S., Chen, Z., He, X.-J.. 2026-09-16. J-domain proteins stimulate PKL-mediated chromatin compaction at H3K4-hypomethylated genomic loci. https://doi.org/10.64898/2026.09.14.751395

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