A5100669407- Epigenetics and DNA Methylation
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- Osteoarthritis Treatment and Mechanisms
- Atrial Fibrillation Management and Outcomes
- Cancer-related molecular mechanisms research
- Congenital heart defects research
- Cancer-related gene regulation
- Pluripotent Stem Cells Research
- Cardiac Arrhythmias and Treatments
- Tissue Engineering and Regenerative Medicine
- Chromosomal and Genetic Variations
- Genetics and Neurodevelopmental Disorders
- Mesenchymal stem cell research
- MicroRNA in disease regulation
- RNA Research and Splicing
- Single-cell and spatial transcriptomics
- Cardiac electrophysiology and arrhythmias
- Renal and related cancers
- Cancer, Lipids, and Metabolism
- Lipoproteins and Cardiovascular Health
- Muscle metabolism and nutrition
- Heat shock proteins research
- Plant Pathogens and Fungal Diseases
- Metabolism and Genetic Disorders
Washington University in St. Louis
2016-2025
Xi'an Jiaotong University
2018-2025
Nantong University
2022-2025
Lanzhou University Second Hospital
2018-2025
Affiliated Hospital of Nantong University
2022-2025
Institute of Hematology & Blood Diseases Hospital
2025
Chinese Academy of Medical Sciences & Peking Union Medical College
2022-2025
Shanghai Cancer Institute
2024
Fudan University Shanghai Cancer Center
2018-2024
Zhejiang Chinese Medical University
2024
The reference human genome sequence set the stage for studies of genetic variation and its association with disease, but epigenomic lack a similar reference. To address this need, NIH Roadmap Epigenomics Consortium generated largest collection so far epigenomes primary cells tissues. Here we describe integrative analysis 111 as part programme, profiled histone modification patterns, DNA accessibility, methylation RNA expression. We establish global maps regulatory elements, define modules...
Here, we introduce the 3D Genome Browser, http://3dgenome.org , which allows users to conveniently explore both their own and over 300 publicly available chromatin interaction data of different types. We design a new binary format for Hi-C that reduces file size by at least magnitude visualize interactions millions base pairs within seconds. Our browser provides multiple methods linking distal cis-regulatory elements with potential target genes. Users can seamlessly integrate thousands other...
Abstract Understanding kidney disease relies on defining the complexity of cell types and states, their associated molecular profiles interactions within tissue neighbourhoods 1 . Here we applied multiple single-cell single-nucleus assays (>400,000 nuclei or cells) spatial imaging technologies to a broad spectrum healthy reference kidneys (45 donors) diseased (48 patients). This has provided high-resolution cellular atlas 51 main types, which include rare previously undescribed...
The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling diverse panel mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state accessibility in developing fetus. In total performed 1,128 immunoprecipitation with sequencing (ChIP-seq) assays histone modifications 132 assay transposase-accessible using...
Naïve human pluripotent stem cells (hPSCs) provide a unique experimental platform of cell fate decisions during pre-implantation development, but their lineage potential remains incompletely characterized. As naïve hPSCs share transcriptional and epigenomic signatures with trophoblast cells, it has been proposed that the state may have enhanced predisposition for differentiation along this extraembryonic lineage. Here we examined isogenic primed hPSCs. We found can directly give rise to...
Neuropathic pain encompasses a diverse array of clinical entities affecting 7-10% the population, which is challenging to adequately treat. Several promising therapeutics derived from molecular discoveries in animal models neuropathic have failed translate following unsuccessful trials suggesting possibility important cellular-level and differences between animals humans. Establishing extent potential laboratory humans, through direct study human tissues and/or cells, likely facilitating...
We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA and proteomics phosphoproteomics profiling, of 218 tumors across 7 histological types childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade (25), medulloblastoma (22), ganglioglioma (18), craniopharyngioma (16), atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span boundaries, suggesting treatments used for one type may be applied...
Aging is a major risk factor in many forms of late-onset neurodegenerative disorders. The ability to recapitulate age-related characteristics human neurons culture will offer unprecedented opportunities study the biological processes underlying neuronal aging. Here, we show that using recently demonstrated microRNA-based cellular reprogramming approach, fibroblasts from postnatal near centenarian donors can be efficiently converted into maintain multiple age-associated signatures....
Abstract Tissue fibrosis and organ dysfunction are hallmarks of age-related diseases including heart failure, but it remains elusive whether there is a common pathway to induce both events. Through single-cell RNA-seq, spatial transcriptomics, genetic perturbation, we elucidate that high-temperature requirement A serine peptidase 3 (Htra3) critical regulator cardiac failure by maintaining the identity quiescent fibroblasts through degrading transforming growth factor-β (TGF-β). Pressure...
DNA methylation plays key roles in diverse biological processes such as X chromosome inactivation, transposable element repression, genomic imprinting, and tissue-specific gene expression. Sequencing-based profiling provides an unprecedented opportunity to map compare complete methylomes. This includes one of the most widely applied technologies for measuring methylation: methylated immunoprecipitation followed by sequencing (MeDIP-seq), coupled with a complementary method,...
Abstract Background Small noncoding RNAs (ncRNAs), including short interfering (siRNAs) and microRNAs (miRNAs), can silence genes at the transcriptional, post-transcriptional or translational level [1, 2]. Results Here, we show that microRNA-10a (miR-10a) targets a homologous DNA region in promoter of hoxd4 gene represses its expression transcriptional level. Mutational analysis miR-10a sequence revealed 3' end miRNA is most critical element for silencing effect. MicroRNA-10a-induced...
Uncovering mechanisms of epigenome evolution is an essential step towards understanding the different cellular phenotypes. While studies have confirmed DNA methylation as a conserved epigenetic mechanism in mammalian development, little known about conservation tissue-specific genome-wide patterns.Using comparative epigenomics approach, we identified and compared patterns rat against those mouse human across three shared tissue types. We that differentially methylated regions are strongly...