Biology subjects

Yuan, D.-Y.

Publications and source records attributed to Yuan, D.-Y..

3 recordsLinked to original sources

bioRxiv2026

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

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.

plant biology↗

bioRxiv2024

The Arabidopsis histone H3K4me3-binding ALFIN-like proteins mediate histone H2A ubiquitination and coordinate diverse chromatin modifications

The histone H3K4 trimethylation (H3K4me3) is widely distributed at numerous actively transcribed protein-coding genes throughout the genome. However, the interplay between H3K4me3 and other chromatin modifications remains poorly understood in plants. In this study, we find that the Arabidopsis thaliana H3K4me3-binding ALFIN-LIKE (AL) proteins are associated with H3K4me3-enriched genes at the whole-genome level. The AL proteins contain a C-terminal PHD finger, which has a conserved role in recognizing H3K4me3, and a PHD-associated AL (PAL) domain, which is responsible for binding to diverse chromatin-related proteins. We demonstrate that the AL proteins not only act as subunits of the Polycomb repressive complex 1 (PRC1) to mediate H2A ubiquitination at H3K4me3-enriched genes but also interact with a variety of other chromatin-related proteins. Furthermore, we elucidate the mechanisms by which AL proteins interact with other chromatin-associated proteins to integrate H3K4me3, H2A ubiquitination, H2A.Z deposition, H3K27 demethylation, and chromatin accessibility across the genome. These findings underscore the critical role of AL proteins in linking H3K4me3 with a variety of other chromatin modifications in plants.

plant biology↗

bioRxiv2024

Co-recognition of histone acetylation and H3K4 trimethylation by GTE4-EML complex in Arabidopsis

Although histone acetylation and H3K4 trimethylation (H3K4me3) are well-known histone marks associated with active transcription, how they cooperate to regulate transcription remains largely unclear in plants. Our study revealed that the Bromodomain and Extra-terminal (BET) protein GTE4 binds to acetylated histone and forms a complex with the redundant H3K4me3-binding EMSY-Likeproteins EML1 or EML2 (EML1/2) in Arabidopsis thaliana. The eml1 eml2 (eml1/2) double mutant exhibited a morphological phenotype similar to the gte4 mutant, and most of the gte4-mediated differentially expressed genes were co-regulated in the eml1/2 mutant. Through chromatin immunoprecipitation followed by deep sequencing (ChIP-seq), we found that GTE4 and EML2 co-occupy protein-coding genes enriched with both histone acetylation and H3K4me3, exhibiting a synergistic effect on the association of the GTE4-EML complex with chromatin. The association of GTE4 with chromatin requires both the Bromodomain and the EML-interacting domain. This study identified a previously uncharacterized complex and uncovered how it cooperatively recognizes histone acetylation and H3K4me3 to facilitate gene transcription at the whole-genome level in Arabidopsis.

molecular biology↗