Guangrun Yu
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View article: H3K4 demethylase SsJMJ11 negatively regulates drought-tolerance responses in sugarcane
H3K4 demethylase SsJMJ11 negatively regulates drought-tolerance responses in sugarcane Open
View article: Dynamic DNA methylation modifications in the cold stress response of cassava
Dynamic DNA methylation modifications in the cold stress response of cassava Open
Cassava, a crucial tropical crop, faces challenges from cold stress, necessitating an exploration of its molecular response. Here, we investigated the role of DNA methylation in moderating the response to moderate cold stress (10 °C) in ca…
View article: Dynamic physiological and transcriptomic changes reveal memory effects of salt stress in maize
Dynamic physiological and transcriptomic changes reveal memory effects of salt stress in maize Open
View article: Histone Maps in Gossypium darwinii Reveal Epigenetic Regulation Drives Subgenome Divergence and Cotton Domestication
Histone Maps in Gossypium darwinii Reveal Epigenetic Regulation Drives Subgenome Divergence and Cotton Domestication Open
The functional annotation of genomes, including chromatin modifications, is essential to understand the intricate architecture of chromatin and the consequential gene regulation. However, such an annotation remains limited for cotton genom…
View article: High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon
High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon Open
Background The adaptation of plants to cold stress involves changes in gene expression profiles that are associated with epigenetic regulation. Although the three-dimensional (3D) genome architecture is considered an important epigenetic r…
View article: Additional file 1 of Dynamic physiological and transcriptomic changes reveal memory effects of salt stress in maize
Additional file 1 of Dynamic physiological and transcriptomic changes reveal memory effects of salt stress in maize Open
Additional file 1: Table S1. Sequencing and mapping statistics for the RNA-seq data.
View article: Additional file 4 of High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon
Additional file 4 of High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon Open
Additional file 4: Table S3. TADs identified at 5 kb resolution.
View article: Additional file 2 of High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon
Additional file 2 of High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon Open
Additional file 2: Table S1. Hi-C data summary.
View article: Additional file 3 of High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon
Additional file 3 of High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon Open
Additional file 3: Table S2. A/B compartments identified at 50 kb resolution.
View article: Additional file 5 of High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon
Additional file 5 of High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon Open
Additional file 5: Table S4. Chromatin loops identified in normal and cold-treated plants.
View article: Additional file 6 of High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon
Additional file 6 of High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon Open
Additional file 6: Table S5. Differential loops were identified between normal and cold-treated plants.
View article: Genome-wide chromatin accessibility analysis unveils open chromatin convergent evolution during polyploidization in cotton
Genome-wide chromatin accessibility analysis unveils open chromatin convergent evolution during polyploidization in cotton Open
Allopolyploidization, resulting in divergent genomes in the same cell, is believed to trigger a “genome shock”, leading to broad genetic and epigenetic changes. However, little is understood about chromatin and gene-expression dynamics as …
View article: Optimization of protoplast isolation, transformation and its application in sugarcane (Saccharum spontaneum L)
Optimization of protoplast isolation, transformation and its application in sugarcane (Saccharum spontaneum L) Open
Sugarcane is a prominent source of sugar and ethanol production. Genetic analysis for trait improvement of sugarcane is greatly hindered by its complex genome, long breeding cycle, and recalcitrance to genetic transformation. The protoplas…
View article: Genome-Wide Characterization of DNase I-Hypersensitive Sites and Cold Response Regulatory Landscapes in Grasses
Genome-Wide Characterization of DNase I-Hypersensitive Sites and Cold Response Regulatory Landscapes in Grasses Open
Deep sequencing of DNase-I treated chromatin (DNase-seq) can be used to identify DNase I-hypersensitive sites (DHSs) and facilitates genome-scale mining of de novo cis-regulatory DNA elements. Here, we adapted DNase-seq to generate genome-…
View article: Optimization of Mature Embryo-Based Tissue Culture and Agrobacterium-Mediated Transformation in Model Grass Brachypodium distachyon
Optimization of Mature Embryo-Based Tissue Culture and Agrobacterium-Mediated Transformation in Model Grass Brachypodium distachyon Open
Agrobacterium-mediated genetic transformation is well established in the model grass Brachypodium distachyon. However, most protocols employ immature embryos because of their better regenerative capacity. A major problem associated with th…