A5015436281- Molecular Biology Techniques and Applications
- Epigenetics and DNA Methylation
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Single-cell and spatial transcriptomics
- DNA and Nucleic Acid Chemistry
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Advanced biosensing and bioanalysis techniques
- Gene expression and cancer classification
- Biological Stains and Phytochemicals
- Genetic Syndromes and Imprinting
- Folate and B Vitamins Research
- Environmental DNA in Biodiversity Studies
- Neurogenesis and neuroplasticity mechanisms
- Bamboo properties and applications
- Neuroinflammation and Neurodegeneration Mechanisms
- Microbial Natural Products and Biosynthesis
- Genomics and Chromatin Dynamics
- Bioinformatics and Genomic Networks
- Cancer Genomics and Diagnostics
- Alzheimer's disease research and treatments
- Nutrition, Genetics, and Disease
- Renal and related cancers
- Biochemical and Molecular Research
Peking University
2015-2025
Center for Life Sciences
2018-2025
Broad Institute
2022-2024
Massachusetts Institute of Technology
2022-2024
Mayo Clinic
2024
Changsha Hospital for Maternal and Child Health Care
2015
Wuhan University
2015
The precise control of messenger RNA (mRNA) translation is a crucial step in posttranscriptional gene regulation cellular physiology. However, it remains challenge to systematically study mRNA at the transcriptomic scale with spatial and single-cell resolution. Here, we report development ribosome-bound mapping (RIBOmap), highly multiplexed three-dimensional situ profiling method detect translatome. RIBOmap 981 genes HeLa cells revealed cell cycle-dependent translational colocalized...
High-resolution detection of genome-wide 5-hydroxymethylcytosine (5hmC) sites small-scale samples remains challenging. Here, we present hmC-CATCH, a bisulfite-free, base-resolution method for the 5hmC. hmC-CATCH is based on selective 5hmC oxidation, chemical labeling and subsequent C-to-T transition during PCR. Requiring only nanoscale input genomic DNA samples, enabled us to detect hydroxymethylome human embryonic stem cells in cost-effective manner. Further application cell-free (cfDNA)...
Abstract 5-Hydroxymethylcytosine (5hmC) is an important epigenetic mark that regulates gene expression. Charting the landscape of 5hmC in human tissues fundamental to understanding its regulatory functions. Here, we systematically profiled whole-genome at single-base resolution for 19 types tissues. We found preferentially decorates bodies and outperforms body 5mC reflecting Approximately one-third peaks are tissue-specific differentially-hydroxymethylated regions (tsDhMRs), which deposited...
Abstract Spatiotemporal regulation of the cellular transcriptome is crucial for proper protein expression and function. However, intricate subcellular dynamics RNA remain obscured due to limitations existing transcriptomics methods. Here, we report TEMPOmap—a method that uncovers profiles across time space at single-cell level. TEMPOmap integrates pulse-chase metabolic labeling with highly multiplexed three-dimensional in situ sequencing simultaneously profile age location individual...
mRNA has recently been established as a new class of therapeutics, due to its programmability and ability produce proteins interest rapidly in vivo. Despite demonstrated utility, protein expression platform remains limited by translational capacity RNA stability. Here, we introduce messenger-oligonucleotide conjugated RNAs (mocRNAs) enable site-specific, robust, modularized encoding chemical modifications for highly efficient stable expression. In mocRNA constructs, chemically synthesized...
DNA methylation and hydroxymethylation are extensively reprogrammed during mammalian early embryogenesis, studying their regulatory functions requires comprehensive maps at base resolution. Here, we develop single-cell 5-hydroxymethylcytosine (5hmC) chemical-assisted C-to-T conversion-enabled sequencing (schmC-CATCH), a method leveraging selective 5hmC labeling for quantitative, base-resolution, genome-wide landscape of the hydroxymethylome in mouse gametes preimplantation embryos spanning...
Spatial omics technologies characterize tissue molecular properties with spatial information, but integrating and comparing data across different modalities is challenging. A comparative analysis tool that can search, match, visualize both similarities differences of features in space multiple samples lacking. To address this, we introduce CAST ( C ross-sample lignment S pa T ial omics), a deep graph neural network (GNN)-based method enabling spatial-to-spatial searching matching at the...
Abstract DNA glycosylases must distinguish the sparse damaged sites from vast expanse of normal bases. However, our understanding nature nucleobase interrogation is still limited. Here, we show that hNEIL1 (human endonuclease VIII-like 1) captures base lesions via two competing states interaction: an activated state commits catalysis and excision repair, a quarantine temporarily separates protects flipped auto-inhibition. The relative dominance depends on key residues chemical properties...
The hippocampus has important roles in learning and memory. Many vivo experiments require accurate location of a certain region the hippocampus, long-term potentiation (LTP) recording being one them. In vitro studies can be used to measure LTP hippocampus. It is more difficult locate specific brain than vitro. Location dentate gyrus (DG) perforant path (PP) usually achieved using stereotaxic atlasses. Because data atlasses were obtained from particular rat/mouse strain (Rat: adult Wistar,...
Abstract The emergence of unnatural DNA bases provides opportunities to demystify the mechanisms by which polymerases faithfully decode chemical information on template. It was previously shown that two cytosine (termed “M‐fC” and “I‐fC”), are labeling adducts epigenetic base 5‐formylcytosine, can induce C‐to‐T transition during amplification. However, how recognize such remains enigmatic. Herein, crystal structures pairing dA/dG in KlenTaq polymerase‐host–guest complex system dATP...
Abstract Amyloid-β plaques and neurofibrillary tau tangles are the neuropathologic hallmarks of Alzheimer’s disease (AD), but spatiotemporal cellular responses molecular mechanisms underlying AD pathophysiology remain poorly understood. Here we introduce STARmap PLUS to simultaneously map single-cell transcriptional states marker proteins in brain tissues mouse models at subcellular resolution (200 nm). This high-resolution spatial transcriptomics revealed a core-shell structure where...
Abstract The precise control of mRNA translation is a crucial step in post-transcriptional gene regulation cellular physiology. However, it remains major challenge to systematically study at the transcriptomic scale with spatial and single-cell resolutions. Here, we report development RIBOmap, three-dimensional (3D) situ profiling method detect for thousands genes simultaneously intact cells tissues. By applying RIBOmap 981 HeLa cells, revealed remarkable dependency on cell-cycle stages...
Summary Spatiotemporal regulation of the cellular transcriptome is crucial for proper protein expression and function 1 . However, intricate subcellular dynamics RNA synthesis, decay, export, translocation remain obscured due to limitations existing transcriptomics methods 2–8 Here, we report a spatiotemporally resolved mapping method (TEMPOmap) uncover profiles across time space at single-cell level in heterogeneous cell populations. TEMPOmap integrates pulse-chase metabolic labeling with...
Abstract The emergence of unnatural DNA bases provides opportunities to demystify the mechanisms by which polymerases faithfully decode chemical information on template. It was previously shown that two cytosine (termed “M‐fC” and “I‐fC”), are labeling adducts epigenetic base 5‐formylcytosine, can induce C‐to‐T transition during amplification. However, how recognize such remains enigmatic. Herein, crystal structures pairing dA/dG in KlenTaq polymerase‐host–guest complex system dATP...