Biology subjects

Shen, W.-H.

Publications and source records attributed to Shen, W.-H..

4 recordsLinked to original sources

bioRxiv2026

The INO80-EEN complex prevents genomic rearrangements at protein coding genes regions

Plants are continuously exposed to a myriad of DNA-damaging agents, including environmental cues such as sunlight. At the cellular level, plants respond to DNA damage by activating DNA damage response (DDR) pathways, in which chromatin remodelers play an important role. Among them, the evolutionary conserved INO80 complex (INO80c) has been shown in Arabidopsis to play a key role in DDR, notably by positively regulating Homologous Recombination (HR). Arabidopsis EIN6 ENHANCER (EEN) is the homolog of Yeast INO EIGHTY SUBUNIT 6 and interacts with the N-terminal region of INO80 in the INO80c. Using plant phenotyping, cellular and molecular biology, and third-generation sequencing technology we investigated how INO80 and EEN regulate plant development and genome integrity. We uncovered new roles for INO80 and EEN in plant growth and for INO80 in fine tuning endoreduplication. In addition, linear genome analysis revealed an important and unexpected function for the INO80-EEN complex in preventing Protein Coding Genes (PCGs) from structural rearrangements in somatic tissue and upon exposure to UV-B. Therefore, our results shed new light on the previously overlooked roles of INO80 and EEN in protecting genome integrity at PCGs.

plant biology↗

bioRxiv2025

The histone methyltransferase SDG26 shapes cold stress responses in Arabidopsis through chromatin-based regulation of ABA-dependent and ABA-independent pathways

Plants constantly face adverse environmental conditions, including temperature drops that can severely impair growth and productivity. To cope with such stresses, they have evolved complex mechanisms of transcriptional reprogramming. While various cold-responsive pathways have been described, the contribution of chromatin-level regulation, and in particular histone modifications, remains largely obscure. Here, we identify the histone methyltransferase SET DOMAIN GROUP 26 (SDG26) as a positive regulator of cold stress responses in Arabidopsis thaliana. We show that SDG26 is transcriptionally induced and post-transcriptionally stabilized by cold, and that its loss of function leads to increased freezing tolerance but reduced drought tolerance. At the molecular level, SDG26 promotes expression of cold-responsive genes, including members of the CBF-COR regulon, through direct binding and histone H3 lysine 36 trimethylation (H3K36me3) at their chromatin. Concomitantly, SDG26 modulates abscisic acid (ABA) biosynthesis, catabolism, and transport, thereby promoting ABA accumulation, stomatal closure, and drought tolerance. Collectively, our results reveal that SDG26 integrates ABA-dependent and ABA-independent pathways to fine-tune Arabidopsis responses to abiotic stresses. We further establish SDG26 as a chromatin modifier contributing to stress-responsive H3K36me3 enrichment at specific loci. Together, our work identifies SDG26 as a chromatin-based hub balancing cold acclimation with water conservation, thereby enhancing plant resilience.

plant biology↗

bioRxiv2025

H3K4me1 directs H3K36me2 and H3K36me3 deposition in land plants

Monomethylation of histone H3 lysine 4 (H3K4me1) marks enhancers in mammals. However, the function of H3K4me1 in plants remains largely unclear. Here, we analyzed the genome-wide distribution of H3K4me1 in diverse species across evolution, revealing a distinctive H3K4me1 distribution pattern in land plants. To explore the function of H3K4me1 in plants, we identified an H3K4me1-specific reader protein, Early heading date 3 (Ehd3), and solved the structure of Ehd3 in complex with the H3K4me1 peptide, revealing a unique binding module differing from the previously reported PHD finger proteins. We further identified an Ehd3-binding protein, SET domain group 724 (SDG724), and the deletion of either Ehd3 or SDG724 caused similar defects in plant phenotype and changes in transcriptome and epigenome profiles. Both Ehd3 and SDG724 are enriched at chromatin regions marked by H3K4me1 but not H3K4me2 or H3K4me3. Ehd3 activates the H3K36 methyltransferase SDG724, and H3K36me2/me3 are colocalized with H3K4me1 in the genomes of land plants. Collectively, our results reveal that H3K4me1 directs the establishment of H3K36me2 and H3K36me3 in land plants.

molecular biology↗

bioRxiv2024

Structural and functional interrelationship of histone H2A and its variants H2A.Z and H2A.W in Arabidopsis

Multiple histone H2A variants are known in eukaryotes. However, the functional relationship between H2A and its variants in plants remains largely obscure. Using CRISPR/Cas9 editing, we generated a mutant lacking four H2A isoforms in Arabidopsis and analyzed the functional and structural relationship between H2A and its variants H2A.Z and H2A.W. RNA-sequencing and phenotype analyses revealed mild changes in gene transcription and plant development in the mutants lacking H2A, H2A.Z, or H2A.W compared with the wild-type plants. Chromatin immunoprecipitation sequencing analysis showed that H2A is able to substitute for both H2A.Z and H2A.W across the genome, including in euchromatin and heterochromatin regions. However, H2A.Z replaced both H2A and H2A.W primarily within the euchromatin regions. By using DNA and histones derived from Arabidopsis, we constructed nucleosomes containing H2A, H2A.Z, or H2A.W and resolved their cryogenic electron microscopy structures at near-atomic resolution. Collectively, the results reveal the structural similarity and functional redundancy of H2A and H2A variants in Arabidopsis.

plant biology↗