A5005011499- Plant Molecular Biology Research
- Genomics and Chromatin Dynamics
- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Wheat and Barley Genetics and Pathology
- Photosynthetic Processes and Mechanisms
- Plant Disease Resistance and Genetics
- Plant Reproductive Biology
- Plant nutrient uptake and metabolism
- Light effects on plants
- Plant-Microbe Interactions and Immunity
- CRISPR and Genetic Engineering
- Soybean genetics and cultivation
- Epigenetics and DNA Methylation
- Single-cell and spatial transcriptomics
- Signaling Pathways in Disease
Huazhong Agricultural University
2015-2025
Institute of Science and Technology Austria
2025
Abstract Epigenomic modifications are instrumental for transcriptional regulation, but comprehensive reference epigenomes remain unexplored in rice. Here, we develop an enhanced chromatin immunoprecipitation (eChIP) approach plants, and generate genome-wide profiling of five histone RNA polymerase II occupancy with it. By integrating accessibility, DNA methylation, transcriptome datasets, construct epigenome landscapes across various tissues 20 representative rice varieties. Approximately...
Abstract Chromatin loops connect regulatory elements to their target genes. They serve as bridges between transcriptional regulation and phenotypic variation in mammals. However, spatial organization of its impact on gene expression plants remain unclear. Here, we characterize epigenetic features active promoter proximal regions candidate distal construct high-resolution chromatin interaction maps for maize via long-read analysis by paired-end tag sequencing (ChIA-PET). The indicate that are...
Auxin response factors (ARFs) are an important family of proteins in auxin-mediated response, with key roles various physiological and biochemical processes. To date, a genome-wide overview the ARF gene citrus was not available. A systematic analysis this begun by carrying out search for homologs ARFs. total 19 nonredundant genes (CiARF) were found validated from sweet orange. comprehensive CiARFs undertaken, including structures, phylogenetic analysis, chromosome locations, conserved motifs...
Abstract Insight into high-resolution three-dimensional genome organization and its effect on transcription remains largely elusive in plants. Here, using a long-read ChIA-PET approach, we map H3K4me3- RNA polymerase II (RNAPII)-associated promoter–promoter interactions H3K9me2-marked heterochromatin at nucleotide/gene resolution rice. The chromatin architecture is separated different independent spatial interacting modules with distinct transcriptional potential covers approximately 82% of...
The complexity of the epigenome landscape and transcriptional regulation is significantly increased during plant polyploidization, which drives genome evolution contributes to adaptability diverse environments. However, a comprehensive map Brassica napus still unavailable. In this study, we performed integrative analysis five histone modifications, RNA polymerase II occupancy, DNA methylation, transcriptomes in two B. lines (2063A B409), established global maps regulatory elements, chromatin...
Chromatin immunoprecipitation with sequencing (ChIP-seq) population cells or tissues yields ensemble epigenomic profiles that only represent the average, which eliminates cell-to-cell epigenetic heterogeneity. immunocleavage (ChIC-seq) (Ku et al., 2019) based on antibody-guided chromatin cleavage under targets is a practical alternative to ChIP-seq. Many single-cell ChIC-based methods, such as scChIC-seq 2019), CUT&Tag (Kaya-Okur CoBATCH (Wang ACT-seq (Carter and 10× scCUT&Tag (Bartosovic...
In response to drought stress (DS), plants undergo complex processes that entail significant transcriptome reprogramming. However, the intricate relationship between dynamic alterations in three-dimensional (3D) genome and modulation of gene co-expression responses remains a relatively unexplored area.
SUMMARY The grains of rice ( Oryza sativa ) are enclosed by a spikelet hull comprising the lemma and palea. Development determines storage capacity grain, thus affecting grain yield quality. Although multiple signaling pathways controlling size have been identified, transcriptional regulatory mechanisms underlying development remain limited. Here, we used RNA‐seq ATAC‐seq to characterize transcription chromatin accessibility dynamics during hulls. A time‐course analysis showed that more than...
N4-methylcytosine (4mC) is an important DNA modification in prokaryotes, but its relevance and even presence eukaryotes have been mysterious. Here we show that spermatogenesis the liverwort Marchantia polymorpha involves two waves of extensive methylation reprogramming. First, 5-methylcytosine (5mC) expands from transposons to entire genome. Notably, second wave installs 4mC throughout genic regions, covering over 50% CG sites sperm. requires a methyltransferase (MpDN4MT1a) specifically...
Characterizing genome-wide histone posttranscriptional modifications and transcriptional factor occupancy is crucial for deciphering their biological functions. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) a powerful method profiling of factor-binding sites. However, the current ChIP-seq experimental procedure in plants requires significant material several days completion. CUT&Tag an alternative low-sample single-cell epigenomic using protein A-Tn5 transposase...
Histone modification H3K27me3 is an important chromatin mark that plays vital roles in repressing expression of developmental genes. Here, we construct high-resolution 3D genome maps using long-read interaction analysis by paired-end tag sequencing (ChIA-PET) and characterize H3K27me3-associated interactions elite rice hybrid, Shanyou 63. We find many H3K27me3-marked regions may function as silencer-like regulatory elements. The elements can come into proximity with distal target genes via...
Photoperiods integrate with the circadian clock to coordinate gene expression rhythms and thus ensure plant fitness environment. Genome-wide characterization comparison of rhythmic genes under different light conditions revealed delayed phase constant darkness (DD) reduced amplitude (LL) in rice. Interestingly, ChIP-seq RNA-seq profiling exhibit synchronous oscillation H3K9ac modifications at their loci long non-coding RNAs (lncRNAs) proximal loci. To investigate how rhythm is regulated...
DNA methylation plays an important role in gene regulation and genomic stability. However, large hypomethylated regions known as valleys (DMVs) or canyons have also been suggested to serve unique regulatory functions, largely unknown rice (Oryza sativa). Here, we describe the DMVs seedlings, which were highly enriched with developmental transcription genes. Further detailed analysis indicated that grand (gDMVs) might be derived from nuclear integrants of organelle (NORGs). Furthermore,...
Epigenetic modifications that exhibit circadian oscillations also promote of gene expression. Brassica napus is a heterozygous polyploid species has undergone distant hybridization and genome doubling events young distinct origin. Studies incorporating rhythm analysis epigenetic can offer new insights into differences in diurnal oscillation behavior among subgenomes the regulation diverse expressions homologous rhythms biological clocks.In this study, we created high-resolution...
Abstract The integration, through hybridization, of the DD genome into domesticated tetraploid wheat gave rise to allohexaploid wheat, most cultivated globally growing across diverse environmental conditions. However, regulatory basis this integration on increased adaptability in remains largely unexplored. Here, we investigated change transcriptome, epigenome as well chromatin interactome, and metabolome three independent polyploidization events representing integration. Our findings reveal...