A5101925686- Plant Molecular Biology Research
- Chromosomal and Genetic Variations
- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- Genetic Associations and Epidemiology
- Genetics and Neurodevelopmental Disorders
- RNA modifications and cancer
- Genetic Mapping and Diversity in Plants and Animals
- Cancer-related molecular mechanisms research
- Genomics and Phylogenetic Studies
- Schizophrenia research and treatment
- Genomic variations and chromosomal abnormalities
- Photosynthetic Processes and Mechanisms
- Plant Reproductive Biology
- MicroRNA in disease regulation
- Bladder and Urothelial Cancer Treatments
- RNA Research and Splicing
- Microbial Natural Products and Biosynthesis
- Blood disorders and treatments
- Plant nutrient uptake and metabolism
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- Plant Disease Resistance and Genetics
- Plant biochemistry and biosynthesis
- Effects and risks of endocrine disrupting chemicals
Huazhong Agricultural University
2011-2025
Chinese Academy of Agricultural Sciences
2023-2025
China Agricultural University
2022-2025
Shanghai Jiao Tong University
2015-2025
Henan University Huaihe Hospital and Huaihe Clinical Institute
2018-2025
Shanghai Mental Health Center
2016-2025
Shanghai Center for Brain Science and Brain-Inspired Technology
2023-2025
Agricultural Genomics Institute at Shenzhen
2023-2025
Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University
2006-2024
Wenzhou Medical University
2006-2024
Cohesin extrusion is thought to play a central role in establishing the architecture of mammalian genomes. However, has not been visualized vivo, and thus, its functional impact energetics are unknown. Using ultra-deep Hi-C, we show that loop domains form by process requires cohesin ATPases. Once formed, however, loops compartments maintained for hours without energy input. Strikingly, ATP, observe emergence hundreds CTCF-independent link regulatory DNA. We also identify architectural...
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 Programmed cell death (PCD) during tapetum degeneration in postmeiotic anthers is critical for the proper development of male gametophytes flowering plants. Although several genes involved this process have been identified recently, molecular mechanism still poorly understood. Here, we show that knockout rice (Oryza sativa) APOPTOSIS INHIBITOR5 (API5), which encodes a putative homolog antiapoptosis protein Api5 animals, results delayed due to inhibition tapetal PCD leading defects...
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...
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...
EndoC-βH1 is emerging as a critical human β cell model to study the genetic and environmental etiologies of (dys)function diabetes. Comprehensive knowledge its molecular landscape lacking, yet required, for effective use this model. Here, we report chromosomal (spectral karyotyping), (genotyping), epigenomic (ChIP-seq ATAC-seq), chromatin interaction (Hi-C Pol2 ChIA-PET), transcriptomic (RNA-seq miRNA-seq) maps EndoC-βH1. Analyses these define known (e.g., PDX1 ISL1) putative PCSK1 mir-375)...
Abstract Background Maize ears and tassels are two separate types of inflorescence which initiated by similar developmental processes but gradually develop distinct architectures. However, coordinated trans cis regulation differentially expressed genes determining ear tassel architecture within the 3D genome context is largely unknown. Results We identify 56,055 52,633 open chromatin regions (OCRs) in developing maize primordia using ATAC-seq characterize combinatorial epigenome features...
Eukaryotic genomes are extensively transcribed into various types of RNAs, many which physically associated with chromatin in cis at their transcription sites or trans to other genomic loci. Emerging roles have been uncovered for these chromatin-associated RNAs (caRNAs) gene regulation and genome organization, yet they remain challenging interrogate. Here, we present TaDRIM-seq, a technique employing Protein G (PG)-Tn5-targeted DNA elements situ proximity ligation concurrently probe caRNAs...
We isolated 13 804 T-DNA flanking sequence tags (FSTs) from a insertion library of rice. A comprehensive analysis the FSTs revealed number features demonstrating highly non-random distribution insertions in rice genome: were biased towards large chromosomes, not only absolute but also relative density; within chromosomes occurred more densely distal ends, and less centromeric regions; was correlated with that full-length cDNAs, correlations heterogeneous among chromosomes; strongly...
Cytokines critically control immune responses, but how regulatory programs are altered to allow T cells differentially respond distinct cytokine stimuli remains poorly understood. Here, we have globally analyzed enhancer elements bound by IL-2-activated STAT5 and IL-21-activated STAT3 in identified Il2ra as the top-ranked gene regulated an STAT5-bound superenhancer one of top genes STAT3-bound superenhancers. Moreover, found that binding was rapidly superenriched at highly induced IL-2...
Genome-wide association and fine-mapping studies in 14 autoimmune diseases (AID) have implicated more than 250 loci one or of these diseases. As 90% AID-associated SNPs are intergenic intronic, pinpointing the causal genes is challenging. We performed a systematic analysis to link 460 that associated with AID using transcriptomic data from 629 blood samples. were able 71 (39%) AID-SNPs two nearby genes, providing evidence for part multiple exist. While 54 shared by AID, 17% them do not share...
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...
Abstract Replication protein A (RPA), a highly conserved single-stranded DNA-binding in eukaryotes, is stable complex comprising three subunits termed RPA1, RPA2, and RPA3. RPA required for multiple processes DNA metabolism such as replication, repair, homologous recombination yeast (Saccharomyces cerevisiae) human. Most eukaryotic organisms, including fungi, insects, vertebrates, have only single gene that encodes each subunit. Arabidopsis (Arabidopsis thaliana) rice (Oryza sativa),...
Meiosis is essential for eukaryotic sexual reproduction and important genetic diversity among individuals. Although a number of genes regulating homologous chromosome pairing synapsis have been identified in the plant kingdom, their molecular basis remains poorly understood. In this study, we novel gene, PAIR3 (HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS 3), required rice. Two independent alleles, designated pair3-1 pair3-2, were our T-DNA insertional mutant library which could not form...