A5070892348- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Cancer Genomics and Diagnostics
- Advanced biosensing and bioanalysis techniques
- Genomics and Phylogenetic Studies
- Single-cell and spatial transcriptomics
- Cancer-related gene regulation
- Analytical chemistry methods development
- Polymer Surface Interaction Studies
- Click Chemistry and Applications
- Electrochemical sensors and biosensors
- DNA and Nucleic Acid Chemistry
- HIV Research and Treatment
- RNA and protein synthesis mechanisms
- Cancer-related molecular mechanisms research
- Carbon and Quantum Dots Applications
- CRISPR and Genetic Engineering
- Prenatal Screening and Diagnostics
- Nanoparticle-Based Drug Delivery
- Molecular Sensors and Ion Detection
- RNA Research and Splicing
- Neuroinflammation and Neurodegeneration Mechanisms
Wuhan University
2024-2025
University of Oxford
2018-2021
Ludwig Cancer Research
2018-2021
Beijing National Laboratory for Molecular Sciences
2013-2016
Peking University
2013-2016
Dana-Farber Cancer Institute
2016
Dana-Farber Brigham Cancer Center
2016
Brigham and Women's Hospital
2016
Harvard University
2016
Abstract We present long-read Tet-assisted pyridine borane sequencing (lrTAPS) for targeted base-resolution of DNA methylation and hydroxymethylation in regions up to 10 kb from nanogram-level input. Compatible with both Oxford Nanopore PacBio Single-Molecule Real-Time (SMRT) sequencing, lrTAPS detects accuracy comparable short-read Illumina but long-range epigenetic phasing. applied sequence difficult-to-map mouse embryonic stem cells identify distinct events the integrated hepatitis B virus genome.
Abstract Although various methods have been developed for sequencing cytosine modifications, it is still challenging specific and quantitative of individual modification at base-resolution. For example, to obtain both true 5-methylcytosine (5mC) 5-hydroxymethylcytosine (5hmC) information, the two major epigenetic usually requires subtraction methods, which increases noise high depth. Recently, we TET-assisted pyridine borane (TAPS) bisulfite-free direct 5mC 5hmC. Here demonstrate that sister...
Novel cell-free DNA whole-genome methylome sequencing method enables accurate cancer detection.
Abstract The analysis of circulating tumour DNA (ctDNA) through minimally invasive liquid biopsies is promising for early multi-cancer detection and monitoring minimal residual disease. Most existing methods focus on targeted deep sequencing, but few integrate multiple data modalities. Here, we develop a methodology ctDNA using (80x) whole-genome TET-Assisted Pyridine Borane Sequencing (TAPS), less destructive approach than bisulphite which permits the simultaneous genomic methylomic data....
Presence of excess unaltered, wild-type (WT) DNA providing no information biological or clinical value often masks rare alterations containing diagnostic therapeutic clues in cancer, prenatal diagnosis, infectious diseases organ transplantation. With the surge high-throughput technologies there is a growing demand for removing unaltered over large pools-of-sequences. Here we present nuclease-assisted minor-allele enrichment with probe-overlap (NaME-PrO), single-step approach broad genome...
Human apurinic/apyrimidinic endonuclease/redox effector factor 1 (APE1) is an essential DNA repair protein.Herein, we demonstrate that avidin-oriented abasic site-containing strands (AP-DNA) on the surface of silica coated magnetic nanoparticles (SiMNP) can selectively respond to APE1 while resist digestion by other nucleases.Mechanism studies have revealed avidin may serve as organizer protein and recruit substrates via strong specific interactions.Taking advantage this newly disclosed...
We demonstrate the successful construction of fluorescently labeled magnetic antibody-like nanoparticles (ANPs) via a facile one-step surface-initiated in situ molecular imprinting approach over silica coated magnetite (Fe3O4@SiO2) core–shell nanocomposites. The as-prepared ANPs had highly compact structure with an overall size 83 ± 5 nm diameter and showed excellent aqueous dispersion stability. With predetermined high specificity to target protein biocompatibility, enabled rapid,...
Aberrant methylation changes, often present in a minor allelic fraction clinical samples such as plasma-circulating DNA (cfDNA), are potentially powerful prognostic and predictive biomarkers human disease including cancer. We report on novel, highly-multiplexed approach to facilitate analysis of clinically useful changes populations. Methylation Specific Nuclease-assisted Minor-allele Enrichment (MS-NaME) employs double-strand-specific nuclease (DSN) remove excess with normal patterns. The...
Abstract Whole genome base-resolution methylome sequencing allows for the most comprehensive analysis of DNA methylation, however, considerable cost often limits its applications. While reduced representation can be an affordable alternative, over 80% CpGs in are not covered. Building on our recently developed TET-assisted pyridine borane (TAPS) method, we here described endonuclease enrichment TAPS (eeTAPS), which utilizes dihydrouracil (DHU)-cleaving digestion TAPS-converted to enrich...
Abstract We report the first direct sequencing methodologies for quantitative detection of 5mC and 5hmC at single-base resolution single-cell level, termed scTAPS (for + 5hmC) scCAPS+ specifically). With ∼90% mapping efficiency, our methods accurately benchmark profiles in CD8+ T mES cells, respectively. Notably, revealed a global increase within hippocampus aging mice, both neurons non-neurons.
Abstract The deamination of unmodified cytosine to uracil by treatment with bisulfite has for decades been the gold standard sequencing epigenetic DNA modifications including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). However, this harsh chemical reaction degrades majority generates libraries low complexity. Here, we present a novel bisulfite-free base-resolution method, TET Assisted Pic-borane Sequencing (TAPS), detection 5mC 5hmC. TAPS relies on mild reactions, detects...